Considering how much Ian was in X2, 2 weeks is incredible.
Then again, Cyke wouldn't need to be in X3 as much as Ian was in X2 for an appropriate role. So in two or three weeks, I don't think filming lots of Cyke stuff would have been too straining. Yeah, some scenes would have to be done with other actors and that would matter, and the Final Battle would be a big issue because I'm sure there was a lot of planning around that - but it could probably done with a green screen, and I think they did pickups laters - I'm sure James could have made it for something like that.
Basically, if Fox was willing to put in the effort, IMHO it could have been done.
Fox was not interested in putting in the effort.