I haven't seen it yet, but having read the previous reviews, then your post, it occurred to me that frequently the problem with movies is conflict between the producer and/or director, who have a certain vision of how to tell the story, and marketing, who has a certain vision on how to sell a movie.
This thread makes me wonder if the first cut of X3 was too long...and the studio forced the producer to cut it to less than 2 hours to make it more marketable.