I too am disappointed by this. 
Other than a comedy or animated film, I don't remember any films that impressed me greatly that were 90 minutes. With the exception of Shrek 2, Finding Nemo, and The Lion King, the top 20 highest grossing domestic films are all over 2 hours. I think people really want to see a good well rounded story to be truly satisfied. 
I mean from what I'm hearing the Transformers are over 2 hours. Do you mean to tell me that Dreamworks can get 2 hours of movie out of the Transformers but FOX can't get 2 hours out of the FF, SS, Doom, and Galactus combined? I've said it before, this smacks of corporate thinking in my opinion. 
90 minutes, more viewings = more $.
DVD Sales = $.
DVD 1.5 Sales = more $.
90 minutes, fits nicely into a 2 hour time slot on Fox Network.
Now let me think about this, I truly do love going to the movies I really do, some movies really do deserve the BIG screen but....
A) I could either plunk down my $9.50 ti see the movie once, overpay for stale popcorn and flat soda, endure an audience with people that won't shut up, or stop kicking my seat, or turn off their cell-phone, or control their kids, to see a movie that was cut up by 25%. 
Or....
B) I could wait and buy the Directors Cut DVD for $15 and see the movie as originally intended with the 25% restored footage whenever I want on my nice home theater system where the popcorn is hot and the soda (or other beverage) is fresh and I can pause to go to the bathroom if I want.
Hmmmm....
Unfortunately, I'll probably do A once, matinee though $6.50, and B. However if it was really good and over 2 hours I would probably do multipe A's as I have done in the past many times.
My $.02. 
IMD