Good question! What I liked about generation 5 is that it was the first one that had a really big city, & utilized the 3d effects of the DS to it's most effect. I also loved the story, especially the part involving Team Plasma. Ghetsis was one of the best organization leaders that I've ever found, & I took great pleasure fighting him in all the games. Everything else is just icing on the cake.
However, the bad things about it are that most of the 'mons are, rather lackluster in my eyes, especially the starters, & that the post-story to me was rather lacking. Sure there was more of the region to explore after the 1337 four, but there wasn't much else to do afterward.
Now, as for my favorite generation, I'm going with the fourth. That generation got everything right in my book.