The Skyway's demise has had perhaps the most outrage and rumor surrounding it of any recent change to the Park, save the infamous reworking of Pirates. The various rumors of its cause range from the completely untrue (some idiot fell out) to the mostly true (Anaheim required wheelchair access and the Matterhorn couldn't be so altered). The truth is more interesting than any of the rumors I've run across.
Whether it was Anaheim's political correctness or Disneyland's that required wheelchair access for all of its transportation (even one as dubious as the Skyway), I'm not sure. The fact of the matter is that wheelchair access was desired or required for the Skyway. Three major changes had to be made to implement this: redesign the cars to accommodate wheelchairs, change the boarding areas from stairways to ramps, and widen the passage through the Matterhorn for the new cars.
The fact is that the Matterhorn is just a big shell at (and above) where the Skyway passed through. Widening the holes was no great problem. The other two adjustments were the tricky bit. As I understand it, the cars have already been redesigned. The Tomorrowland stop was to be moved in the Tomorrowland renovation, so the decision was made to simply remove it altogether until then, and the holes in the Matterhorn were covered for obvious aesthetic reasons. The remaining question is whether the new Skyway will be routed through the Matterhorn again or whether the new terminus' position will allow it. I have no answer for this.
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