X2 hands down.
X2 had more emotion, drama, atmosphere, and better writing in which we(the fans) cared about the characters. Everyone is entitled to their opinions, although I think those who complain about Singer being bland, unoriginal, and boring need to take off their ADD hats and look at the overall product.
There's more to the X-Men than just wonderful eye candy. Of course, X-Men in general is not a realistic entity, then again what comic book movie or comic book in general is realistic?
I think what Singer did that Ratner didn't do was add emotion to it. Singer presented the characters strongly, made us care about them, and helped us understand their yearning to fit in with common society.
From my own personal experience as a comic book fan; I was moved emotionally by seeing Logan hold Rogue in his arms as he thought she was dead. The music, the atmosphere, and the silence between the two really set a mood and made you hope for the best.
In X2, it was painful and very powerful to watch Scott cry in Logans arms when Jean perished. I don't care what anyone says, it was an emotional moment and proved that Marsden is a capable actor.
Fox and Rothman shat on the Dark Phoenix saga and the fact that X3 apologists can defend it shows they'll accept anything.
There are a lot of emotional moments obviously. Moments that really struck a chord and made a very powerful impact. Ratner, while he didn't create a trainwreck by any means, he didn't really allow a moment in the film to breathe or allow the impact to settle in. It was just Xavier is dead, Cyclops is dead, let's not mourn or anything let's just go on pretening that nothing happened. Example of bad writing:
Logan- ::See's Scotts glasses floating::
Storm- LOGAN!!!
Logan- Jean?
See anything wrong with that? Where's the "Oh, by the way, I found Scotts glasses. Let's look around for him."
Or better yet
"Professor, I found Scotts glasses. Perhaps you should use cerebro to try and find him?"
The lack of character development, bad writing, bad ADD directing, and no emotional heart is what really made this film suffer. Now in defense of Ratner, I will say that this film should've been a Uwe Boll film. Given the studio politics, the rushed filming production, and etc, etc....This film should've been an absolute trainwreck and the fact that it wasn't warrants Ratner quite a bit of respect.
But other than that, it's the only credit he will receive. It doesn't change the fact that Ratner, Penn, and Kinberg are studio yes-men.
X3 allowed no development. Fox screwed Singer on including Beast, Juggernaut, and Gambit for X2 with the limited budget he received. You know how many times I had to roll my eyes because the audience wondered, "Why is that big blue guy acting like he's so intelligent?"
If given more time with better writers and directors, this film could've provided some back history for Beast, Juggernaut, more Colossus time, and possibly introduce Gambit as well.
The only good things about X3 was McKellen, Marsden, Grammer, Janssen, and Stewart.
There is a reason why Spider-Man 1/2, Batman(1989), Batman Begins, Superman 1/2, V For Vendetta, X1/X2, Sin City, Blade 1/2, and Hellboy are respected among the comic book/non-fan community. They were given a lot of time to flesh out ideas, studios didn't barge in to ruin a great concept, and the directors took their time rather than flat out admitting, "I get bored very easily on the set, so I immediately move to the next scene after the first take."