A heavier flywheel will *reduce* the vibration (you can never actually stop it, just make it really small).  It won't shift the problem up or down the rev-range.
The throttle response Rick mentions will be most noticable on how long the engine takes to spin down between gear changes.  I don't expect it to be a problem at all, but if you want to count the half seconds, you might be able to spot it.
Take a look at the size of the flywheel on the industrial 4BG1T for the extreme example.  For an engine that just runs at one rpm, bigger is better.  Drawing here, look at the section view:  
http://www.isuzu.co.jp/world/product...f/b_draw02.pdf