After X2's length, the running time is a clear issue the film had. I blame that on the script more than Ratner. Ratner shot the script they had.
I'd say a key problem (and it was a bad movie all around) was the rather ridiculous Jean Wolverine love "thing".
Let's review, shall we? In X-Men Wolverine meets Jean when he first comes to the institute. He briefly talks to her. And after that, they don't interact much if any, at least not in any significant way, until near the end. One scene. Then he leaves. He doesn't return until the beginning of the next movie. He sees a glimpse of her. They don't interact until right before the climax of the movie, which is implied to be very brief. And then she... "dies". The next time they meet, oh yeah, they're doomed lovers.
Wolverine is first attracted to, and later has deeper feelings for Jean.
She doesn't love him in return. This is made clear in X2. She is attracted to him, as she was in the comics. This is made clear as well.
When she gets busy with him in X3, it is Dark Phoenix taking over.
There is never a doomed lovers triangle, only Wolverine being forced to kill the woman he loves to save everyone.
Could be that, or it could be a weak, rushed film. I don't hate it like some do, but it's obviously inferior to the previous 2 films.
Except that it's not. Not in any measurable sense. It's shot differently. The acting is on the same level. The writing is on a similar level, with a bit more comic book flair, and a few corny lines/moments, which all the movies had. But the writing also has more character development, varied exploration of key themes and comic book mythos in it than previous films did.
The action is nice, but emotional underpinnings throughout are underwhelming and half baked. Angel exists in a couple of scenes and is ultimately irrelevent to the plot. Rogue's decision to take the cure is totally squashed by her jealousy of Iceman and Kitty, and what should be a serious life choice comes off as being about "some boy". Halle Berry is terrible. Logan's story is incredibly dry, assuming a dull hero role. Any motivation for Pyro's anger is glossed over and he's just an ass who now hates Iceman. The death of Cyclops is simply lost in the shuffle. Xavier's death gets a little more attention but is undermined by the fact that he nothing of note prior to it (aside from cussing out Logan in a very out of character moment).
The emotions being underwhelming is your opinion. Half baked is your opinion. They're not any more or less underwhelming or half-baked than the previous movies. The emotional elements are structurally and contentwise handled as well, or better, than the previous films did. The only emotional aspect of the film that is not handled as well is the team's reaction to Cyclops' death. And given the circumstances, not pausing for a funeral is understandable. We do, however, get to see Jean's reaction to Cyclops death, and its an appropriately emotional and powerful one. The death of Cyclops is not neccessarily los i n the shuffle so much as it is one of the major events in the film. They don't return to it a lot, but they do acknowledge it, and the impact of it, several times.
Halle Berry isn't terrible. For once. She's actually better than she was in either of the two previous films. She should probably never have been Storm in the first place, but she's at her best in the franchise in X3.
Angel exists in a few scenes, much the way Bobby and Pyro existed in a few scenes in X2. Angel is most certainly not irrelevant to the plot. He is a shining example of a mutant who might want the cure, and chooses not to take it.
I don't know how you can call Logan's role "dull". He goes around killing people, just like he always does. He does some tracking. He has several meatier dialogue scenes, including a nice sequence with Rogue. He's got emotional sequences...and he has a very cool action/healing sequence toward the end of the film. Dull? Really?
Pyro's anger was only ever about jealousy and Magneto telling him he can be more than humans in X2. A sense of superiority. That is all still very present in X3. And he was always an ass. Right from the start.
Xavier's death is one of the best comic book movie sequences ever. It gets more than a "little more attention". And he does have sequences of note prior to it. He has a teaching sequence, the moment with Storm, the scene with Wolverine about Jean, the sequence between himself, Jean and Eric. And Xavier never cusses out Logan...what the heck are you talking about? Xavier manipulating people is not out of character in the least. He's done it for two films. It is simply revealed that this is what happened with Jean, and that his tactics are on a while other level. It was, to most fans, a welcome addition to the film universe.
Why do you even bother to list "problems" with the film if they're, as you stated earlier, halfbaked?