I think your takes are quite valid, but I took things very differently. While they were overused I mostly loved the escort and stealth quests in the MSQ because they gave me a much closer experience to the story than just running to orange zone after orange zone.

I knew the whole time we'd be getting the scions back, but that didn't undercut the sentiment for me in the ending. I also really liked the Garlean zone stuff, I think it really captured the themes of struggling to move on. They were blatantly stupid as fuck that is true, but in a way I found very human rather than just plot stupid. (There is a bit of plot stupidity though, I felt like Hades and Hermes in Elpis reacted to Meteions report very strangely given the circumstances.)

Absolutely agree on Ultima Thule and Omega. It was obvious from the outset. The same is true of the Moon and Y'shtola revealing the rabbits benefactor is the forum. Obviously the devs know we can figure it out so if there needs to be a moment of 'revelation' at least let us bring it up since we've been aching to point it out since getting to those zones.