The only thing that makes me kinda regret not liking In Hushed Whispers as gated plot quest in DA:I

That first part is kind of what I mean. With IHW, you get a very clear picture of how things end up without the Inquisitor (or, more aptly at that point, I guess, the Herald). However, you don't really find out much about the how of it. You know Celene dies, but not that there's a distinct plan to assassinate her. You know "the Elder One" unleashed demons, but not that he had a faction of people actually summoning demons for the purpose of it. You get more of those things by playing CotJ, although that means that in exchange, you don't get the benefit of knowing the degree of threat that those plans really signify.

To disband the Templars is tempting stuff, yes.

The Inquisitor doesn't go to Redcliffe to bind an alliance with Tevinter, but because Fiona invited his/her, while the Templars refused the offer (it hard to forget!). And when the Inquisitor already arrives in Redcliffe, sees, that the mages are in trouble. It seems, that Fiona's a reluctant ally, not really agree with Alexius, and the situation is weird. Yes, the Inquisitor can leave them, but what expects from the Templars?

There are parts of Champions of the Just that I really like, but I think In Hushed Whispers works so much more for the narrative for a few reasons, primarily because the introduction of odd Tevinter mages practically taking over Redcliffe just seems like super bad juju that needs to be investigated, and that’s always introduced first. 

The Inquisitor can believe or not, what Felix and Dorian say, but the situation still weird, and jeopardizes not only the mages, but the whole Redcliffe, and perhaps more.

Anyway, your arguments are well founded, this is undeniable, and perhaps, I will able to start a run, where I will go for Templars and disband them. I see, there some reasons for it, but to leave Redcliffe still seems a bad idea.

(But I suppose, the Mage-Templar war and the Dalish clans were treated poorly and illogically in the Inquisition, especially the Mages, and Fiona and the three-mages-nonsense, what not really consistent.)

I think the real problem is that the mage rebellion was originally meant to have been a DLC sequel to the events of DA2. It actually merited its own separate story rather then integrating it into Inquisition. Then the mages being in Ferelden would make more sense as the rebellion began in Kirkwall and Alistair, if King, has already been shown in DA2 as sympathetic to their cause, so crossing the narrow stretch of the Waking Sea there would make sense. Presumably the original idea would be that Hawke would either have been leading the mages in their defence or leading the Templars in tracking them down. At the very least the issues could have been dealt with far better than they were.

The issues were more complex than were covered in DAI and, as I've already stated, it made little sense that the mages, who had been placed up on the border between northern Orlais and Tevinter in Asunder, would cross hundreds of miles, fighting past Templars the whole way, plus through the Orlesian Civil War, simply because the monarch of Ferelden had offered them safe haven and the Divine wanted a peace conference, particularly as in the book Fiona had said "F**k the Divine". Mages had already had to travel from all over Thedas to reach Andoral's Reach and it is stated that they could easily withstand a siege there even if vastly outnumbered (assuming of course they could lay in sufficient supplies of food) as it was very defensible.

We also had the fact that Hawke was brought in only when we discovered about Corypheus. Would Varric really not have informed Hawke about the Peace Conference and Hawke declined to get involved, particularly if Anders is still alive and they favoured mage freedom? So the action was completely detached from DA2, something that had been set up in the novel Asunder.

I think the issues behind the Orlesian Civil War were not really dealt with properly in game either. Both these scenarios, that had been set up in novels, really required you to have read the novels to understand what was going on and their resolution felt rushed. So really DAI was trying to cover too much ground in too short a time. Then we discover that then main plot of DAI, the creation of the Breach by magical artefact, had not really been resolved at all because the real culprit had not been identified in the main game and then after he had in the DLC, it was "to be continued".

Possibly, although I like to think that neither Anders nor Hawke would favour throwing their lot in with the Venatori. More likely they would have intervened and stopped the majority of the mages going anywhere near Ferelden anyway.

I forgot to mention that holding the Peace Conference at Haven made no real sense either. It was far too inaccessible for people allegedly travelling from across Thedas and in view of the Orlesian Civil War alone, made it dangerous as well as difficult to get to. Why not the Grand Cathedral in Val Rouyeax if it had to be a site with religious significance? Or simply somewhere in northern Orlais or Nevarra? With the Mortalitasi having far more influence in their country than other mages had in theirs and the original meeting place of the College of Enchanters being in Cumberland, why not hold it there? Instead people were required to travel to an inaccessible mountain location in southern Thedas which was a site that had only been discovered to be of significant to Andrastrians 10 years earlier and where the main reason for this (the Ashes) had already been removed (by the Guardian). Besides whilst the Templars might have been impressed by the location, why would the mages necessarily agree to it?

We can't forget that it's been 10 years since Haven was discovered and it quickly became a place of pilgrimage. Getting there may not have been a walk in the park, but it wasn't inaccessible.

The temple that held ashes of Andraste is a site of tremendous religious significance - way beyond Grand Cathedral in Val Royeaux.

Also: neutral ground (also relatively unfamiliar to anyone). And one that rogue mages and unruly templars would be way more willing to travel to than a seat of power of Orlesian Empire that has also likely retained enough army to pose threat for either side.

I mean, nevermind that in case something happened, like negotiations falling apart and mages/templars engaged in open conflict, remote location guaranteed that any magical shenanigans were far away from harming civilians.

In fact 'magical shenaningans' indeed happened and literally wiped the Temple from existence and left a gaping hole in the sky that was endlessly spewing demons!

Needless to say, one can certainly see sense as to why Conclave has been chosen to happen in a remote location, ways from any significant routes or population. Considering the uncommon volatility of both sides, isolation is wholly advised.

Isn’t the Fiona that we meet in Val Roseau’s clearly not the same as the one in redcliffe. I’ve always assumed time magic was involved based on the rift outside of redcliffe and the soldier telling us we weren’t expected. Dorian tells us that Alexis used time magic to conscript the mages. He’s been basically trying multiple time jumps to change outcome/save Felix but the rift prevents him from stopping it
I believe he uses the time jump as bill Murray did in Groundhog Day. Basically he tricks Fiona in one timeline and uses her again in another
In regards to the conclave. Early earth history has examples of people doing this

The second quote basically answers the first. It would seem that apparently Redcliffe was able to operate in a completely separate time bubble to the rest of Thedas. So Fiona went to Val Royeaux, invited us to Redcliffe and returned there. After this, Alexius wound back time to just after the explosion when the mages were panicking they would be blamed for it, suggested a way out and Fiona found that the majority of her followers were willing to go along with it, partly because the mage rebellion had already been infiltrated by Venatori agents. That's how it was presented to us anyway.

However, if Fiona had been willing to travel to Val Royeaux in order to try and make contact with the Inquisitor, this shows that the mages were still holding out hope of negotiating with the Inquisition even though they knew Templars might come after them at any time. She was also able to travel from Redcliffe Castle to Val Royeaux apparently with little trouble, a not inconsiderable distance. So the idea that when Alexius turned up she felt so desperate she simply accepted his offer does not really hold water. Plus, we have the problem of the time bubble that means everything still had to happen as we experienced it or we would never have met Fiona to receive her offer.

That whole business would have been better explained without the use of time magic. Alexius turned up after the explosion, Fiona was panicking, he made an offer but she still preferred to try an approach to the Inquisitor first. Alexius was happy to go along with this because he wanted the Inquisitor invited to Redcliffe. When we get there, Fiona remembers our meeting and says she has a new ally whom she wishes to include in negotiations. The timing still seems fishy, Dorian and Felix can still warn us that Alexius is in with a bad crowd, some of the mages can still express concern at their new ally and we find the tranquil skulls. So everything is pretty much the same to justify an alliance and deal with a foreign power having taken over Redcliffe Castle but minus the time magic.

Then when we get to the meeting in the Castle, Alexius tries to use his amulet on us, which is now a total surprise, except to Dorian who manages to alter the outcome. We get burped into the future and have to try and return ourselves to the point where the anomaly happened. At least that way we do not have the multiple time-lines problem associated with the earlier time magic use. Unfortunately, even in the future sequence they create further problems with multiple time-lines because the diary makes it clear that Alexius continued to repeatedly try and return to before the explosion occurred. Every time he does this, he is creating a new time line and yet somehow we are still conveniently within it. Not to mention we travel in space as well as time because we ought to have appeared in his throne room yet for some strange reason we end up in the dungeon.

This use of time magic is not the same as that in the ruins within the Western Approach and in Jaws of Hakkon. There people just got trapped in their own time bubble in suspended animation whilst everything went on in the world around them. When we break into the time bubble they then carry on where they left off. It is not ideal but it is better than the events at the beginning of IHW.

Exactly. Then how did she invite us to Redcliffe Castle? This paradox had caused all sorts of theories, such as it was the Envy Demon impersonating her, when it was made quite clear to us, by Dorian, that it was the real Fiona who met us but that subsequently Alexius altered time so to Fiona the meeting never occurred. Except they then have her rubbing her head as though she ought to remember it but doesn't, which would suggest blood magic mind manipulation (perfectly logical considering who we are dealing with) instead of time magic manipulation.

Essentially the writers thought it would be cool to introduce time magic into then plot so that IHW could be substantially different to CoJ where we have the normal Fade sequence with everything happening in our mind. They could have done this with IHW, with the dark future just being something that has been created in Alexius' mind (possibly by the Nightmare demon), which is how we know what is going to happen, but they clearly decided time travel was the way to go. Strangely enough, Solas even questions us on our return and asks if it "could have been a trick of the Fade" and disapproves if you say, "Dorian doesn't think so", but is okay if you say you are sure. So I prefer to think it was a trick of the Fade in which Dorian and I had a joint experience rather than time magic that just befuddles me because it is so full of paradoxes.

Fiona's presence in Val Royeaux only really became mysterious because she had no recollection of it when we got to Redcliffe. Time magic was used to explain her amnesia and decision to sign up with Alexius after inviting the Inquisitor to visit.

Mind you, it would seem as though she was stalking the Inquisitor. How did she know we were travelling to Val Royeaux? It would seem she must have had spies in the Inquisition herself.

As you say, Fiona's story was manipulated to service the time magic plot which then led to more problems with the use of time magic in the setting rather than less. Essentially, though, that part of the plot wasn't necessary. As I outline above, Alexius could simply turn up at Redcliffe after she returned from Val Royeaux and have persuaded her to sign up with him. After all, she had seen what went down with Lucius and the Templars and may have feared that an all out assault on Redcliffe Castle would shortly follow. No need for convoluted time magic plot to explain her change of heart at all.

Anyway, now that there is no Breach I had been confident that would be the last we had seen of time travel magic. However, it is true that they used a form of time manipulation in the Western Approach which set the scene for the same sort of use of magic in Jaws of Hakkon, so I hope that time travel isn't going to feature again anytime soon.

(I should have been more specific back there - the mystery of Fiona's presence was there to set up the time magic. It's just a regular meeting until it turns out that it didn't actually happen.)

Talking about whether time travel was"necessary" is just confused. Time travel wasn't introduced because it was necessary, or helpful, or solved a plot proble. It was introduced because they thought it would be fun. (Didn't find it fun? Well, you've got CotJ.)