Well, of course, X3 promised us a huge amount - Beast, Angel, Danger Room, a more gutsy Storm, Magneto's war, Dark Phoenix. That's a helluva lot to deliver in one movie. Some things were bound to be less fully achieved than others.
By contrast, X1 and X2 never really promised us anything. Disappointment is less when the promises are less. X1 and X2 never promised anything epic, in fact the plot of X1 is totally made-up for the movie. X2 gave us Nightcrawler, a Phoenix subplot and a Deathstrike cameo. Neither of the first two movies said they'd give us anything epic, climactic or world-shattering.
In X3, I thought Beast was brilliantly done - we saw all the necessary elements of the character (all that was missing was him hunched over test-tubes in a lab... and that could have been done as part of his visit to the cure facility, but never mind...). Angel was also very well done, perhaps with too brief an arc for some. The Danger Room served several purposes but the execution of the sequence and the Sentinel didn't succeed entirely (It needed more going on in it, and more work done on it). Dark Phoenix and Magneto's war were fairly well done, but not perfect.
Bryan Singer did so much set-up in the previous movies, hinting at things like Magneto's war and Phoenix, that the third movie had an almost impossible amount to achieve and deliver. It was never going to be 100% successful with all the elements it included. I'm still glad we got to see Beast and Angel and new baddies like Juggernaut, Callisto, Arclight and Multiple Man. Phoenix was fine until the part between marching on Alcatraz and finally freaking out on the island - she did and said nothing in that time to indicate feelings, motivations, doubts, conflicts, turmoils.
I'm sure the pressure is great on writers who are adapting existing material with a devoted fanbase. You're never going to please everyone.