Post game content?

Fair enough.

Funny, that Nihilus moment in particular I think was important. It gives you an early opportunity to think about what kind of Shepard you want to be in the stance towards aliens. If you talked to Preslay before, you already have the background on the turians and the first contact war. Now, you get to decide if Shepard is one to still resent them somewhat (and therefore be rather dismissive) or someone who engages into a conversation with the alien and is interested in other viewpoints. It's subtle but it's there and whenever I replay the game, I notice sthose situations where dialogue was very deliberately planted in the story to give the player the opportunity to shape not just Shepard but their own view of Shepard and refine what kind of character they head canon while playing. Because they couldn't have all actual lines in the game be different or have grand concequences for obvious reasons, they use these small moments to tease the players imagination and thus shape their interpretation of the more general lines alter.
Maybe I am imagining this and give the writers too much credit and it's all coincidence (I have no proof either way) but after at least 15+ playthroughs of ME1 over the last 10 years I am pretty sure a lot of this was deliverate (and brilliant) design.

As for the order of investigation options not always working, this is true in a few cases, definitely.

No, I reject that. I was always for getting rid of the P/R system for Andromeda but I certainly never wanted this. I really didn't expect it either. I mean, say what you will about Inquisition but they did the dialogue wheel without a one-dimensional morality system already and they made it so that the Inquisitor could still say and do different things and express different opinions depending on the wheel choice. In that sense, ME:A is a massive step backward from what DA:I already did pretty well. And a DA:I like situation was what I wanted (and advertised in the old forums a lot). where the writers could use the wheel pretty much to their hearts contempt and put into it whatever they wanted, depending on what the situation required. You know, if it is reasonable that you could get pissed at a squad mate for something they just did or said (looking at you Liam) put that in the wheel somewhere, if it's just as feasible to make a joke about it, do that and so on. Sure, it would have required more diverse responses from the NPCs to what you said (as opposed to now where Ryder effectively always says the same thing so the NPCs only need one response to that) but then, rather make it 3 options again usually, instead of 4 or cut some of that (IMO rather useless) Nomad banter instead. I mean, I don't even want huge concequences here either, I just want to be able to express a feasibly fitting opinion with my character. I also don't expect them to hit exactly what I want to say every single time but the fact that basically every BW game before this one did a better job at this makes ME:A very disappointing to me in that aspect.