If you are a playboater, then take the playboat. I wouldn't have wanted to be in anything other than the boat I normally use during the season for class 3-4 water....which is the playboat. Comfort is obviously an issue but boat speed won't matter too much because the rafts will be the bottleneck in the progress you make down the river each day. Our trip last fall was at 8300 csf and I don't think there were many waves that I missed due to boat size. That being said, we had plenty of room available on the rafts so we were often in the raft anyways during the flatwater. If you don't have this luxury then perhaps a medium sized do-it-all downriver boat would be the way to go so that you'd be more comfortable.
Must do hikes: Thunder river, matkatamiba, elves chasm...check the thread from last fall for other's picks....