First two are definitely my favorites in the series. With Alter Code F I just wished they really tried to remake it rather than borrowing a lot from the Wild Arms 3 engine. Just couldn't take the characters seriously with the expressions they had in the remake. Besides thought the way you learned Fast Draws (from observing and thinking) was better than finding mystical swords. There were good things in the remake, but still prefer the original game.
Would be nice for the 2nd game to get a remake though. Could turn out pretty nice.
First and second game are my favorites. Of course you can't beat that, the gameplay and music of old WA titles are eternal. Although I did appreciate the Alter Code remake, and would like to see 2nd game having one in the near future.