Like many people who had the pleasure of experiencing Alien Encounter, I enjoyed and appreciated that attraction because it was thrilling and intense, without having to be a big elaborate coaster (many of which I can't ride because of motion sickness).
For those who never experienced AE, it's difficult for them to understand how much fun it was. It was an adrenaline rush. It was truly frightening and intense.
Truth be told, it probably did not belong in the MK to begin with. It would have been better suited for the Studios, but it would have needed a more TV/Movie specific theme to align with the then-still-in-tact park identity.
I would be a hypocrite if I said it belonged in the MK, and that it should have stayed there, because I firmly believe the attractions in the MK should accommodate as many demographics as possible (family rides). I don't feel that way about the other parks.
For those of us who were childless young adults when they converted the attraction, it was a serious blow to our enjoyment levels. It went from intense to downright silly. And at the same time, guests were being inundated with Stitch (sort of like with Frozen now) - and enough was enough. "Ruining" a great attraction with something many people weren't fond of just left a bad taste in people's mouths.
If the attraction is around for a few more years, I'll be able to take my new son on it. I'll be able to re-live it through the eyes of a child, and will likely have a new appreciation for it. Meanwhile, I'll continue to dislike the current version of the attraction.