I've owned many types of boats in my lifetime and I see that pontoons are getting somewhat of a bum rap by grouping them all together. Yes many pontoons do not handle rough water as good as others. Most older pontoons had smaller diameter logs and were lower in the water. Also most were underpowered and never got "on plane". Newer pontoons, especially tri-toons handle much larger loads, horsepower and speed and you can drive around in smooth comfort and not get wet (except when its very choppy and windy). I have a 25-foot tri-toon (Bennington--great!). Poeple are always amazed when approaching large wakes and always flinch, only to slice through them without any noticeable boat movement. I would recommend getting one with three 25-inch diameter pontoons for max "lift" (floatation) to be able to handle the rougher water. You also want to watch your loading as most people like to sit up front, but if it's rough, you'll want to distribute more weight aft to avoid waves over the front deck. Don't under-power it. Get at least 100hp to get it on plane and be able to cruise without constant wide-open-throttle (I'm running with 130 hp).
There are also available canvas "cabin" enclosures that can be put up in cooler, wetter weather and are recommended in Spring and Fall because pontoons don't have windshields for the passengers.
I also have a smaller bowrider that I use for "shuttle" duty to/from the island with just the two of us, but I always pick up my guests in style in the pontoon. The pontoon makes a perfect cruising boat and we NEVER get any pounding....even when out for 4th of July fireworks!