Things that don't make sense (v2)

It's mentioned in the game as being an interpretation of quarians based on Shepard's experience with them.  Shepard only knows them as suited and so sees them that way in the data files.  I think one of the quarians sounds like Tali, too.  That's the in-game explanation but ultimately fails since those are video files.

Also, still can't get past that line when they look at the Harbinger fragment in Bryson's lab:
Shepard: "Aren't you afraid of indoctrination?"
Ann Bryson: "It's completely shielded and we've all undergone regular psyche evals."

What?!? you've developed shielding that also works against reaper indoctrination? Even worse, the dialogue implies that they had the fragment basically since the end of ME1. Maybe someone should have given this amazing tech to Amanda Kenson and everyone else who was indoctrinated.

Does this mean that Shepard was or was not indoctrinated?  I discount any meeting with Sovereign since none of it was done face-to-face. 

Unfortunately, your graphic didn't show up.     Anyway, since the plot didn't say it happened I assume it didn't.

It's so bad, it becomes a problem for me to motivate myself to even do quests because I have no sympathy whatsoever for these idiots.

Me neither! Screw the extra xp, I was not going to waste my time helping them.

Anyway, back to things that don't make sense, why isn't Kaidan (or Ashley) taken onto the Collector Ship from Horizon? He/she are one of the first to be bitten by the swarmers. This is not explained well by the events shown in the cut scenes. I am certain this has been discussed before but I searched for an answer here to no avail...

It would have been interesting to rescue them along with the rest of the crew during the Suicide Mission with the bonus of eliminating their shitty attitude at the start of ME3.

Well, no, I don't think any person with common sense would join up but for that matter the initiative should never ever have happened. But I covered that in a post back during my first playthrough in March, so I didn't want to reopen that can of worms.
What I do think is that anyone to be sent on such a venture would be trained for an extended period of time, not just thrown into a cryo chamber with no more than what's in the brochure. That goes double for those top 1% they'd wake up in this emergency situation they are in and triple for those forerunners on the Nexus. I don't even want to think about what the other 19.500 people are like that aren't qualified enough to be woken up yet.

The point is that you basically ask any member of the initiative why they joined, it's almost always a conversation option and all of them have different reasons for joining. It's great that they added this background for all major NPCs but the problem is that every single reason I have heard so far is invalidated by the fact that you could have done all this stuff in the Milky Way. The thrill seekers, the low lives, the escapees, all of them could have headed somewhere in the MW just as easily. The terminus systems are lawless and free of council intervention and 99% of the entire place is completely unexplored as it is. If ODSY drive is a reality, we are no longer bound by clusters and even if we were, back in the Milky Way, humanity has interstellar space flight for a total of 30 years. Most humans would probably hardly ever have seen an alien.
Remember that young C-Sec officer, you can meet in the wards in ME1? He was a thrill seeker. That's why he went to the Citadel, to - and I quote - "meet all sorts of cool aliens. Wild!" That's about 18 months before the Arks take of and the Citadel is about the most civilized part of the MW there is. Want more of a frontier spirit? Go to Trebin and help set up rain clouds or go to one of the Terminus colonies. Want to explore more? Head out into all those uncharted systems in the Attican Traverse. Shepard alone visits dozens of cool uncharted worlds to explore and get lost on.

But in the parallel ME Universe of Andromeda, the doctor who had a midlife crisis, the school teacher who "could predict it all" and the transsexual who just wanted to get away from her old community so no one would call her by her old name, they all decided that they needed to leave the entire galaxy behind and go on a crazy trip of no return.

I could understand the other races, who've been around longer a bit better but even with them it's weird. There is the asari sociologist who runs the cultural center on the Nexus who tells us that "all the books about all the species in the MW have already been written". Hallo? The humans are around for 30 years, which in asari time is nothing. The Yaag have only been discovered recently as well and that's just the tip of the iceberg.

They just all seem like petulant children who think they had a great idea while actually going on a hail marry mission for no rational reason whatsoever.
Oh and by the by, reading some of the codex stuff and the texts from the forward stations, yea, they knew (because of that crazy geth FTL telescope thing) there were garden worlds which they wanted to colonize. However, clearly, they weren't able to pick up whether or not there would already be someone living there. Hawarl for example was classified as an Initiative habitat, so was Voeld, although at the time billions of Angara were already living there. If you look at the MW galaxy map, you'll see that basically every garden world is either having a civilization on it or is claimed by one. So, did they expect it to be different in Andromeda? Or did they fully expect they had to invade and fight the natives for their worlds? Because it is very clear, the Arks and the Nexus were not built to sustain themselves without a foothold on a garden world. In fact, the AI got super lucky with the Angara who are super nice to us (especially given their past). You think the Alliance would just have permitted some wandering aliens a chunk of land to build an outpost on Eden Prime, Terra Nova, Benning and Earth (Hawarl is the Earth of the Angara)? Especially if those aliens basically showed up during our first contact war with the turians?

No man, the initiative was a half cocked venture full of crazy people if you ask me.

So yea, that got out of hand, better not get me started on this, it just boggles my mind too much.