Why an new Alien Encounter can work today
Again, the original Alien Encounter may have been too advanced for the time in storyline and the tech. In the mid-90s, Disney wasn't as much into thrills, more classic family entertainment and folks just weren't ready for the experience.
Today, it's different as audiences are more attuned, especially younger folks who would enjoy something with a lot more spark than the original attractions or Stitch. There's also how the Alien franchise has a lot more appeal than some knock-off creations, and audiences would be inclined to accept it with all of Disney's other IPs.
All they'd have to do is change the company to Weyland Yutani, a new storyline and then update the old Great Movie Ride AA for a new time. There can be a mix of it with screen tech, the hint of other Xenomorphs about and enhancing the in-theater effects. Throw in some 3-D stuff too or even a variation of the original idea of guests trying to blast the alien somehow. Or it can be Disney making it more of a show with actors as "Marines" trying to hunt the Xenomorph down only for them to get picked off.
That creature just calls out to people, designed like something out of a primal nightmare. It's why it's been so captivating for decades and frankly past time it was showcased in a theme park. It might as well be like this as the alien hunting the audience throws them into the story like a classic theme park attraction should.
It just seems inevitable that Disney will use the franchise in some way, given their past history with it and the reliance today on putting IP in parks. It'd be ironic if Michael Eisner's vision, once considered too graphic and off-putting, is now far more accepted and Disney reminding folks just why the Alien franchise has been so perfect in sci-fi scares for so many decades.