My experience has all been with Cataraft, a small Idaho company that was one of the first, and a PAC 800. It does seem that the popularity is consistent with geography and availability. PAC is popular on the West Coast because they are a division of Aire, a company that has made white water rafts and cats for years. The PAC is well made and has as good a pedigree as any on the market.
As far as shoals go, it will depend. Inflatables are terrible if you have to attempt sliding over rocks, but do all right on gravel. They do draft more water however because the footprint is smaller than a kayak or canoe. As far as class goes, the biggest worry on our streams are new strainers and for a pontoon narrow places with trees, etc. If you learn to handle one properly, you have more maneuvering power with oars than with a paddle, which can be a plus.
The capacity of inflatables is generally given as point where the tubes approach the halfway point in submersion and 25% is generally ideal all around. This gives you good tracking, but the ability to maneuver. An overloaded pontoon is a barge and something you defiantly want to avoid if you have to maneuver at all.