This is pretty hard for me, because I really enjoyed all three of the movies, I watched them when I was younger, and recently I bought all three of them on DVD (Had to get a bootleg of Mothra 3 unfortunately.) and I have a new appreciation for them now.
I'm going to have to go with 3, since it was the most enjoyable for me, with the first coming in at second, and the second movie coming in last (Although I still like it a lot.) these movies are vastly underrated, although I hated the ridiculous environmental message in the first couple of movies, the kids were pretty annoying in all three movies, it was especially annoying in the third movie when the kid wouldn't go to school and his parents didn't seem to care, and then the ever infinitely wise sister said one of her friends cried whenever she ate at school because they didn't give her food she wanted, and she said "Is it healthy for children to always eat what they hate?" or some crap like that with the parents standing there like idiots with no answer, it just really ticked me off.
But the real reason why I like these movies is the monster action and boy oh boy do they deliver on monster action, I have always loved Mothra so these movies made me love Mothra even more, it just has the most awesome incarnation ever.
As for the Heisei Gamera movies, which although I enjoyed I found to be largely boring with the monster fights being few and far between, yeah so they made the movies darker, and more "adult" who cares? it's especially disappointing in Revenge of Iris with all its "plot" and "character development" that it skimps on the monster fights, what's there is fantastic, but it just isn't enough for a movie supposedly about Gamera, and he doesn't even use the chest cannon that he did in the Legion movie making it even more lame (Yeah great a glowing hand, way to improve on the last movie there
), so yes I like the Heisei Gamera movies but I feel they are pretty overrated (I was really expecting a lot more with how much people were praising them.), and the Mothra movies just gave me a much better warmer feeling and more excitement.
But enough about Gamera, I prefer Mothra 3 since it has the best strongest Mothra, and the best most awesome Ghidorah so far, there are certain things I like more about each movie, but the third one has the most for me to enjoy.