Retcons or contradictions that you have noticed

One thing worth noting is the types of people who would embark on such a mission. Think of the major (non forced) colonization movements in human history. They were led by either imperialist ambition or by outcasts migrating from societal conditions they do not find acceptable and wanting to start from scratch (or the combination of the two factors). So while forced migrations tended to represent the entirety of the people that had to migrate (for obvious reasons), the colonization and willing migrations tend to only attract certain types of individuals.

Based on the fact that the galaxy at large did not accept Reaper story by the time of departure, the population of colonization ships probably does not represent the population of MW races very well. There are more adventurous types, more outcasts who felt they did not fit in their society and people running from their past. This should in part explain why we are not seeing the same societal structures we saw in MW galaxy. Heck Turian Ark was supposedly constructed without knowledge of Turian Hierarchy, so it is not exactly fair to expect the established class structures surviving on the Arks.

The imperialist ambition is also present in the Ai, and based on the hints dropped about the Benefactors who likely had ulterior motives for this initiative (be it Cerberus or whatever other evil shadow organization BW came up with).

Note, the above does not mean that I do not find the contradictions with established lore jarring. I do. But above helps me rationalize them...somewhat.

Not so much for the physics issues. Those I just have to tune out, as I won't be able to enjoy the game. So every time I read something that is obviously not working the way it would, I just do a little "It's space magic. SPACE. MAGIC." chant and move on.

Would you call a lesbian mom a father IRL? That's your answer. No one would. Human females and Asari do not provide additonal genetic information.
That's not how the reproduction of those species work in the Real World nor how it works in the game. The species on earth who are all female, basically clone themselves, BW just added the randomization of genes with the "father" so there is at least a puprose for Asari to make out with other species. 

To quote Matriarch Aethyta "You anthropocentric bag of dicks"! Just because this is the case for humans (btw not always), Aethyta makes it bluntly clear that this isn't the case for Asari. She calls herself father and Liara calls her dad, while elsewhere she is still refered to with female pronouns.

One things that stumps me is, that did we not need either mass effect relays to jump to diffrent systems in the ME1-3 or at least a bigger ship..
In helius, even though you got explain why the Angaran did not be able to stay in contact since the Kett destroyed their nave and all major ships.
Still rookar can jump through systems with their small shuttles, even Ark ppl could jump several systems fleeing in shuttles. Or Dr.Kennedy who fly around at least 12 systems/ half helius in her shuttle.

But is not Aya and Voeld diffrent clusters? Or Kadara and Nexus in diffrent clusters?

That is the thing. "Father" for them is NOT a male term. Even if Femshep and Liara had a child, Shep would be the "father" from the Asari perspective.

Would you call a lesbian mom a father IRL? That's your answer. No one would. Human females and Asari do not provide additonal genetic information.
That's not how the reproduction of those species work in the Real World nor how it works in the game. The species on earth who are all female, basically clone themselves, BW just added the randomization of genes with the "father" so there is at least a puprose for Asari to make out with other species. 

Oh man, where do I start?!?

I mean, I kinda like the game on it's own but they should have made this a new IP or a reboot or a parallel universe or something because it just doesn't fit into the ME universe as we knew it at all (and I say this despite the fact that I usually despise reboots and parallel universes and that sort of thing).

Let's start with the premise: Why go to Andromeda? In 2185 1% of the Milky Way is explored. You don't need to be 600 years in cryo and take the most stupid-ass risk in history to get a fresh start or satisfy your inner urge to explore at that point. I am not through the game yet and maybe there is some secret reason (I am just saying: reapers) that would make this more believable but even if there is, the whole "fresh start/pioneer spirit" thing seems to be motivation for most low level people you can ask and that already makes no sense.
This by the way is also a problem while playing because to me, all those people in the AI aren't brave, they are simply stupid. For example, when we arrive at the Nexus and are supposed to be like "Oh noooo, this can't be happening!!!", I was outright laughing at them thinking "You idiots!!! This was so completely unnecessary and stupid, you deserve what you got." (and if I think my own protagonist is stupid, it doesn't help with identification wither(.

Then, there is the technology they used: An ODSY drive would have made a HUGE difference for the original trilogy plot. Not only could the Milky Way people have outmaneuvered the reapers to some extent, who clearly don't have that technology. The bigger problem is that even the faint possibility to cross dark space and travel to other galaxies makes the reapers' cycle of extinction scheme a complete and utter joke. "Yea, we'll keep the Milky Way in check with the cycles and if synthetics develop in other galaxies, where they are a couple of billion years ahead of us in development because we just hibernate and do the same shit all over again every 50.000 years without progress, I am sure it'll be fine" It's even more BS now than it used to be. And Shepard doesn't even mention this (well, it wasn't retconned yet at the time, right?).

Tech Nr. 2: SAM. SAM is a complete and utter violation of council rules on A.I. but all four council races built one without the council stepping in? Did they keep it secret? Oh, I am sure the council didn't mind them building "SAM nodes" into their dreadnought sized ARK ships without supervision or control. Governments usually don't care, right? Oh and what about a bunch of private investors building a space station almost as big as the Citadel itself just like that within 10 years that is also capable of flying to another galaxy? I am sure that was easy.

Timelines: When the Andromeda Initiative was founded, humans had interstellar space flight for just over 20 years. and first contact happened 15 years before. Yet, a private human businesswoman has the cloud to start the most ambitious undertaking in the history of at the very least this reaper cycle (if not all cycles) as a multilateral cooperative endeavor evolving almost all MW species. She did this despite the fact that the other species and their galactic economies are millenia older and more advanced? I mean, the ME timeline was always shoddy at best but this brings it to a whole other level.

They take Krogan to Andromeda and try to cure the genophage (by trying to run gene therapy during cryosleep, which is complete BS on its own but ok). I mean, I am sure the salarians and turians on the initiative were thrilled about that idea, right?


I could go one for ages like this, those are just some points from the top of my head.
While I do agree that the Asari male thing is just stupid and takes away from the species' interest factor, at least they just decided to call themselves something different, I can worl with that even if I think it was unnecessary and stupid.
I do not buy some of the fundamental premises of this setup though and while I do really like the game itself, I'll never be able to play it without some measure of contempt because of those issues.

I am not entirely through the story yet but if they don't come up with something absolutely amazing at some point, calling this Mass Effect is a bit of a farce.

I'm affirming their non concept of gender. That was literally the point of my post. Suddenly we have 'male asari' when they had no concept of gender a year ago within the culture of the ME universe. I wasn't trying to say that the 'father' is a father in the RL sense; I was saying that the series was using it as shorthand for 'non-birthing biological parent who did not fertilize the mother'.

I would say that the gene randomization counts as giving genetic information in a sense. The asari mother uses the other parent's genetics as a map for randomizing the genes, or something along those lines.

We essentially agree. I think it's a difference of phrasing.

That's not true. They don't provide genetic information. It's simply not true.

The father helps randomize the genes with space magic.
Why is it relevant? Because there is no biological reason to call them father's.

Bw made them father's to underline their non concept of gender.

I love how normalized inconsistency and retconning has become for this brand.

"Mac Walters lives and breathes Mass Effect like it's nobody's business" - John Dombrow

I agree, John. He truly, truly does. He's defined its identity in a sense.