The Lugia movie is certainly in my top 3 of the movies, but looking back with an objective eye, Mewtwo Strikes Back and Spell of the Unown aren't really up there.
As for the animation, Pokemon the Movie Black and White are incredible in that regard; particularly the opening credits battles, which are just on a totally different level to what we've seen before.
As for Destiny Deoxys, it was much better than I remembered it. The CGI is hilariously awful, and the music is really pretty bad (apart from Deoxys' little tubular bells motif- that's really nice), but Watch Da Birdie nails it talking about the sense of tension and dread; that scene with the Deoxys tentacles coming through the air vents probably traumatised a generation of kids. Only the Groudon bits of Jirachi Wishmaker and the tree bits of Lucario and the Mystery of Mew come close.
Lucario and the Mystery of Mew is still just on a totally different level to the rest of the movies, though; backstory, scale, emotion, action, the lot.