The Prestige is a better film than TDK (or BB for that matter), and probably better than TDKR as well (still need to see TDKR before judging). So yeah, it's not like RT is perfect at judging the quality of films. Matter of fact, history is littered with films that weren't universally acclaimed at first but became more appreciated over time.
What's interesting to me about TDKR is the constant, I meant constant references to Ledger's Joker. Not even in the movie and still having an impact on this movie. I have to see it myself, but I'm not convinced it's getting an entirely fair shake if people are comparing it to TDK and wanting another Heath Joker. The Batman fans who have seen it seem to be gushing a lot of praise for the fact that it ties back in so well with BB. Critics might not give a damn about that aspect of it, but I sure do.