It's hard to decide really. I guess it all depends on what I focus most on when I think about the three. For characterization, X1 is the one for me (except for Storm). When I look back at the films now, I see how drastically the characterizations changed from one to three. I miss the consistancy. It is obvious that the writers were not the same, it shows. For Storm and Wolverine it shows almost a 180 degree turn. For Storm for the better and for Wolverine for the worse. I miss the X1 Wolverine and Rogue and I welcome the X3 Storm.
When I think of story line, X2 and X3 are running neck and neck. Both stories (and I emphasize stories) are intriguing and interesting and have multiple layers to them. In X1, the story falls a bit flat and really serves as introduction for the characters.
Action? X3 hands down. Nearly the entire time between X2 and X3, people have stated they want more more more. More mutants, more carnage and more destruction. We got that finally. Body count, destruction and mayhem. X2 lacked that, and the action was more localized and more intimate.
So for me X1 wins for characterization, X2 for its "moments" (Nightcrawler in the White House, Wolverine vs. Deathstrike, Jean vs. the water etc) and X3 for full blown action.
Each film has its problems, each has it high points. For each of the above I mentioned what worked and what clicked for me.