It's not so much that prestige classes bother me, but that we will be roughly doubling the rate of level advancement in roughly the same amount of game hours as the first KotOR.
I don't think we'll need to worry so much about balance. Prestige classes will make our characters powerful enough as it is, but going level 30-40 will ummm....more than offset any ummm...balance issues.
Basically, we'll be too powerful.