based on my years on the board (and my own experiences riding it), it boils down to these reasons:
a) it's a watered-down version of an attraction that was much beloved by many park goers, especially those that frequent these boards.
b) it doesn't have a repeatability factor to it. you could argue alien encounter did, because you wanted to see how others reacted to that suspense, or relive those tense moments. with stitch, that element is taken away. so once you ride it, why would you again?
c) some people just don't like stitch.
d) there's some residual anger towards stitch from when the company tried to force feed him in the early 2000s (an attempt to lump him into the iconic fab 5, inclusion in the monorail spiel, TPing the castle).
if they would have gutted the inside and given stitch a more original attraction, i could see some people not being to opposed to it. but when you walk in there, you can still feel the ghost of alien encounter, replaced by a character some find to be very irritating.
personally, i like stitch. i think he's fun. loved the movie. but i can't stand this attraction. not necessarily for all the reasons i gave you, but i feel pangs of some in my resentment toward the ride.