Spoilers ahead

The quest to find Amelia makes zero sense, as I'd already become leader as this point: there was no option to say to the scientist 'hey, actually I'm with the Institute, I'm gonna kill you and take back your synths'. At the very least, I would have liked an option to reclaim Amelia if she were indeed a synth.

I think this is the only quest I've found so far that isn't fitting in with my personal storyline though.

If you're aligned with the Institute, wiping out Covenant and the Compound would be the natural reaction. The research they did would be useful to the programmers though. Without knowing the ID of the synth, you don't have a recall code though.

Mm, I get that, but if you kept her in your cell and got an option to return to the institute to check it out you could do it that way - it would have been nice to have an actual dialogue option to say something along those lines to the female scientist at the end: 'I'm reclaiming this synth' or something like that ;D

Bethesda games are notorious for not caring what rank you are in a faction when doing things like this.

Yeah, that's why Preston Garvey thinks it is ok to order the general around like he was a lowly private....... Seems to me, the GENERAL LEADS, not gets ordered around.....

https://s-media-cache-ak0.pinimg.com/564x/4a/08/11/4a0811dce3246a5050d243ad050c7010.jpg

OT: Yea I wish Beth let us go around with special dialogue options depending on who we are. Would've been cool to have Covenant be friendly to a BOS Knight SS since they both hate Synths.

I suppose when Bethesda had this quest in mind they wrote it as if its relatively early in the game, where it makes the most sense to ask those questions about what a synth is in dialogue and your typical boogeyman responses. Makes less sense the further you are into the game.

Guess it's another oversight from Bethesda.