I feel like X3 and X1 were the only ones set up as real x-men "adventures", where they fought together as a team. While it was cool seeing everyone split up at the end of X2 to do whatever, I'd rather see that happen here and there and not often in the films. And for the first time in the trilogy, I felt we saw a big-scale (dare I say, epic) battle- X-Men theme and all.
Something I applaud Ratner for- which his creative team DOES deserve credit for- is that X3 brought the mutant conflict out into the world by incorporating a very powerful, controversial, social issue with the Cure- this was the first film where we saw the world reacting to mutants, threatened by them, trying to help them, etc. X1 and X2 focused just on the X-Men and the Brotherhood(s), with no 3rd party forces or anything brought into the fold. X3 had the X-Men fighting on a national (if not international) battlefield.
Plus, X3 set up Trask and Moira with talented actors, and found a good Multiple Man for 2 scenes. Atleast for Moira and Trask, these weren't cameos, these are seeds for future prominent roles.