Beaker, I should have known that after years of waiting for this movie, that when it came out, you would be ungrateful.
All you can do is complain about what was NOT in the film and say "the film could have been better"? Read that again out-loud.
That's gratitude for you.
This is nothing special, every movie ever made has had scenes cut out of the final product. Besides the running time, they most likely had other reasons for making the cuts.
Any and every movie could be better, even the best of films. Sure, I shudder to think what would make TMM and GMC better... but certainly improvements across the board with most of the other films. Some were quite good as they were, but could have used something. There are movies that an alternate take or extra sequence can make all the difference. Look at how Lucas keeps fussing over the Star Wars films. Adding scenes, changing scenes, adding characters... it all changes context of the films (though, in this case, they weren't for the better).
I loved the film greatly, and find it the best post-Henson Muppet project out there... but even then, I agree... there were some great scenes and concepts lost in the final cut that would have made the movie shine all the more brightly. Like I always say, there's no problem in The Muppets that couldn't be resolved with more movie, and who amongst us wouldn't have wanted more movie? Why else do you think I'm fuming over the deleted scenes being Blu-exclusive?
Personally, I still don't see why a minute's worth of Tex's song needed to be cut. In that minute, everything was explained, it would have helped the ending which came off a little nonsequitor and perhaps a might rushed. Instead, we got punchlines to a set up that didn't exist. Now, I'm not going to pan the movie for one lost scene (unless it's MFS, but that was the director's fault), but it would have turned an A film into an A + for me.