For me, the best movies were the Hoenn Movies and 2000. Manaphy, Jirachi, and Lucario. Those are by far my favorite. Not only are Manaphy and Jirachi just good story wise, they also focused on May and Max. None of the movies focus on other characters, but Ash, but Ash still saves the the day. 2000 was just an extremly epic movie. 4 Legends fighting it out like crazy, almost destroying the entire Orange Islands. And Lucario just had an extremely good story in my opinion.
And I also loved the Hoopa movie. I know a lot of people don't like it, but I loved seeing all of the Legends battling in a Royal Rumble. Lugia kinda got screwed, which was the downside of the movie. But seeing Ash command Rayquaza, Latios and Latias at the same time was just amazing to me.