Out of all the critically acclaimed games I've played over the past several console generations (and on PC), I can think of only one game that really sticks out that did not click for me at all. Grand Theft Auto IV. The whole thing felt very uninteresting and some things annoyed me. Traded it in after playing for 10 hours or so.
Fez may join my list, but I don't feel I've given it enough playtime. Same with Shadow of Mordor. And Xenoblade Chronicles X. Need to put more time into those games.
Uncharted series - the games themselves did click with me, but Drake himself not so much...I thought he was just OK. I liked his supporting cast (Sully, Chloe, Elena, etc) more...for some of them a lot more.
If this thread were created a month or so ago, I may have added Salt & Sanctuary to my list. It was immediately clear to me that the game was pretty well-made, but the first 4 or so areas, the combat, enemies, bosses, art direction, etc didn't really grab me. Fortunately once I got further in, the game really grew on me and now I enjoy it quite a bit. (The patch that added HUD/UI scaling also helped.)
My list of critically acclaimed games that DID click for me but I felt were still a bit overrated for one reason or another is a lot longer. Bioshock, Zelda: Skyward Sword, Final Fantasy VIII to name a few.