It really doesn't bother me that much as I'm now playing through as a Guardian (rebel full) and Shaper (shaper full). So I'll get the endings with those two. As for the one original Agent one, it's a bit annoying not being able to finish at all (even an "bad" non sided ending like you could it 1 and 2), but I had fun and I'll probably play agent again as it's my favorite.
As for the wanting to do the opposite, I found 2 was the best because you had 4 sides to choose from (or choose to not side). Here you really just have 2 and that seems like a big step back. A bit disappointed about that. I really though Khryyk (or whatever his name is on Gull in the West) would be a 3rd option, that's why I chose not to kill him. Unfortunately, it didn't work as he just ended up being part of the shaper side despite having non shaper views.