Well theres two answers. One is they need to stop building only head liners. And or advertising them as such.
I don't think they have a choice anymore. I think one of the key issues here, part of the reason the models are failing, is that the disparity between headliners and non-headliners is widening. Rather than there really being a range of experiences (A, B, C, D and E), everything is getting boiled down into "must-do" or "skip." That's putting way more pressure on the headliners to perform in a way that traditionally they were never meant to.
Case in point: Muppet's still being empty when all those attractions went down yesterday. People are so driven to get the headliners done, that waiting in a 100+ minute wait for Tower of Terror seems like a better option then wasting any time visiting Muppets or seeing a show.
Now everything i said is based off of the EXPECTATION of resonsble and or acceptable crowd levels. Disney is clearly perfectly fine bottoming out the parks capacity. Thus they might not even see the problem because to them it dosen't exsist the level of crowding and line waiting to them MAY BE perfectly acceptable. If thats the case everything i said above is moot.
Well I think another angle on this is that, ultimately, people would rather wait in long lines than be excluded from visiting. My solution would be a simple price increase across the board to curb demand and reduce the overall wait time everywhere. For Disney though that's a terrible solution because pricing people out would have a greater negative impact on the brand image than long wait times.
Secondarily, if attendance was brought back down, you would see a lot of attraction demand dry up, to the point that Disney would be forced to close a lot of their older, more historical attractions. That's not really something I think anyone wants, and especially not Disney. In a weird way, having a 90+ minute wait for Mine Train, justifies keeping Tiki Room and Country Bears around for another year.