Quite a few...
Mystique - She did have big parts,but she could have been given more important parts.
Rogue - Didn't seem like she was part of much after the 1st movie.
Iceman - He did have big parts in X3,but I think that they could have used him alot more.
Colossus - Not shown enough,and he didn't have exciting scenes.
Beast - When everyone saw the X3 trailer and saw beast,they were like,"AWESOME!!!!" and they expected some kick a#% scenes,but..We didn't see Beast in action til towards the end of the film,AND it wasn't even all that much action,I think IMO it was a let down.
Other than Wolverine,Magneto and Xavier I think at some point any one character got the shaft. If it wasn't in screen time,then it was just the on screen portrayal. Most the villains are simply subjugated to henchman status. Most the good guys ended up being background noise.
As much as I enjoy Jackman as Wolverine, through most the trilogy I got the feeling he was the only character capable of offensive action other than Magneto.
I feel personally first class did a better job of navigating this than the first three movies.
If I wasn't a fan of the comics I could only wonder what my impressions of Cyclops would have been. I would have to imagine non-comic fans watching these films would of had the idea this character is for some reason suppose to be important for some unexplained reason.