To respond directly to the OP's post...
I've ridden Voyage for the last three seasons and it has definitely gotten worse. It's still really fun - it just beats you up in the process. It jackhammers in the back, but it's still more fun than painful in the front. As some people have said, I think the timberliners will really help, as I know Holiday World has tried retracking. The forces are just ridiculous on that ride, and the PTCs only seem to be making worse and worse...
El Toro is still ridiculously smooth, but it seems to skip the track on the first turn around once or twice, which is jolting when you're not expecting it. It seems to only be in the back, though.
As for GCIs, I've gotten on Prowler, Term-...I mean, Apocalypse, American Thunder, Thunderhead, Lightning Racer, Wildcat, and Roar. Roar is by and far the worst, and I always try to look at the bright side of wooden coasters. That being said though, I don't think Wildcat is unbearably rough as many do, and all of the newer ones (2000 to now) are not noticeably rough.
And to all the posters that wrote those explanation on rough track, thanks! That was seriously enlightening!