It seems to me that X3 and Spidey 3 had similar problems of cramming too many plots into their running times and sacrificing things like story and character, which both part-2's handled well.
I think one reason this happens is that contracts usually call for 3 movies to be made, and by the time the 3rd film comes around, the filmmakers take it on like it's going to be the last one, so they have to fill the quota and get in the cool stories like the phoenix saga or the black costume in there along with everything else.
So, the way I see it, stop trying to put a cap on the third film. If you want your audience begging for more, it shouldn't be because they want to make up for a crappy part three.
(Come to think of it, isn't that why they made Ocean's 13?)