Cases are what wear. The big bearring wobbles out the race, but still the cause is the crank out of clock or whatever its called. Some call it trueing the crank, but from what I understand from previous posts, assembling the crank right, reduces vibration in a certain rpm range, but is never truely "balanced" And it was also mentioned the the majority of cranks are out. Check out Stewarts Crank Press Thread. You think all engine shops have one of those? Think he and his Dad made that for a good reason? I think it is a big deal, but not an easy fix.
Handlebars and rubber mounting helps symptoms, not the cause. Cases are too expensive.
Your really talking about two different things here, first you can align your crank and that will help immensely, second you can have it balanced, and your right it does reduce vibration in a certain range, the unfortunate thing is since it is a single cylinder motor you can't make it silky smooth all through the RPM range. Alignment helps a bunch.
