I loved Chrono Crusade but I hated the end. It made me cry.
The end to Gravitation just made me go O.o. I love the anime, but the ending is alot clearer in the manga.
Trinity Blood. Ok, the original writer or was it the artist
died, but couldn't they come up with something better than that? They left alot unexplained and unresolved.
I'm sure there are some more, as I'm always complaining about an ending, but that's all I can think of right now.