Used to see hexagon-shaped pontoons - seems like everyone has gone back to round pontoons or U-shaped now. I'd prefer flat-bottom pontoons similar to the hexagon ones - they would get you on plane with a lot less power. I suppose mfrs. went back to round ones because they are cheaper, and if $$ is not an issue they can sell you a bigger motor to make up for lack of performance.
The custom aluminum guys will build pontoon boats with flat-bottom tubes. I think Clark Boats up in Bellevue, IA will build pontoons with rectangular tubes up to 42 inches wide. If I were in the market for a pontoon boat that I planned to keep for a while, I'd check into something like that.
The U-shaped pontoons do have more reserve buoyancy than the round ones. However, buy your boat based on quality, not shape of pontoons, as I've heard some of the boats with the U-shapes did have some flexing/noise issues.
I also think pontoon tubes should be tapered in the back, like a canoe. Since most of your time is spent putt-putting around, tapered tubes would be a lot more efficient. Put planing strakes on them to regain any planing forces lost.