Having spent a considerable amount of time in all shapes and sizes of boats I have come to the conclusion that the #1 most versatile fishing boat is a 16' jon boat. It will do it all and last forever. Customize it a little to suit your needs, and if your needs change you can re-customize it. Or hell, Own two....or THREE for the cost of one factory rigged boat.
I currently have a 16' Lowe Olympic(wide Mod-V) set up as a flyfishing boat with uncluttered decks, and I have a 16' Lowe 1636 (plain ol'jon) for smaller water/rivers. And when/if I sell them I will definately make money.
While it's true that really rough water is gonna be sketchy.....How much time do you really want to spend fishing in (or driving through) 3-4' rollers? Even if your boat can handle it you'll be avoiding water like that anyway unless you compete in big money events regularly, or you're the type of guy that has to fish the opposite end of the lake from where you launch from.