Well, the main reason the Matterhorn is so rough is first and foremost that they designed it on the fly and bent the track pieces out in the field instead of in a warehouse. You don't have the precision of a computer model. Also they designed it to not have banks (or at least sharp banks) on the turns, similar to how a mouse coaster (like Goofy's Sky School) is. This was to add more thrill, but at the expense of more jerky and sudden movement. Most coasters have banked turns to keep things smoother.
I've always felt like they could help with the roughness by adding better shock-absorbtion technology to the vehicles themselves. I'm not sure if that would be too expensive or make the vehicles too bulky or heavy. I'd be fine with a tear-down and rebuild as long as the design was the same, but you can't really "fix" the non-banked lateral turns without changing the feel of the ride. Some sort of lateral dampers in the vehicles would at least alleviate some of the neck pain. Sudden drops could be smoothed out though, as that's what's causing the spinal compression horrors. No amount of padding is going to get rid of that!
