I could blame Season 4 on Pierce's decline, but you're right. He was already on the outs in Season 3, it just wasn't as noticeable because the writing for him was still there.
So I watched the last two episodes of the season back to back. More to get ready for Season 5 tomorrow, and also just to get it over with (I don't hate Season 4, but I'll get to my feelings on it as a whole in a bit).
This episode was really fun, though it did start out a little slow (at least for me), and the ending with "fake" Pierce took me out of the episode a bit, but I really liked what they were going for, showing us that the Study group was always meant to be, and I loved how 'Don't You Forget about Me' was playing over the final scene, I'm always a sucker for that song.
'Advanced Introductions to Finality'
I mentioned earlier on that I was looking forward to this episode because it dealt more with the Darkest Timeline, and I wasn't disappointed, well kind of. I felt the third act with paintball was pretty weak, even with the cute line: "We found a way to make Paint Ball cool again." When it wasn't really "not cool" in the first place. Not to mention the scenes involving the evil Study group hunting the good study group down didn't even come close to the other two (or three I suppose) Paintball episodes.
So a few thoughts on Season 4: I never cared for Annie in this season, she had a few good moments (especially towards the end) but I never really saw her as the same character that she was in the other seasons. Pierce either, though I'll blame that one on Chase and give the show runners a break on this point. He wasn't interested in being there and you were right: Borgified Corpse, that lead to the writers really not being able to write for him.
Also, I wrote down the names of the episodes that I enjoyed and I am surprised to see that out of the 13 episodes I can say that I really enjoyed 9 of them, that's too bad actually. But (and yeah, I'm going there) this isn't Harmon's Community, and while I know I should judge the episodes on their merits (and I am) it's just hard to get by the fact that the show is a shadow of itself. And I know while a lot of people can name several episodes from Harmon's show that they dislike, I can't say I dislike a single episode. There might be some here or there that I find weaker, but I always find something to enjoy (I'll put that to the test when I rewatch Season 5's 'App Development and Condiments' an episode that I struggled to make it through the first time I watched it.