I tend to like the first three movies (and the Mewtwo special, it was pretty fun) better than the ones afterwards (even though I do like time-travel). The others just don't seem to be as great for me.
Why? I like the storylines, I guess. The Pokemon in them were pretty cool as well :3
If I had to pick one, I guess the third. I liked the Unown, and what they created. ^^;
I haven't seen a Pokemon movie in ages though. I think the last one I saw was when they showed the 7th on TV. @_@ I own 4-6, but like I said, they don't appeal to me as much. That, and I just don't watch movies too often anymore unless everyone else wants to watch them.
*should really see about buying the first three someday*