I used to fish Sydney harbor (Australia), Montezuma Slough (San Francisco Bay), the Sacramento-San Joaquin Delta, and various Northern California bass lakes out of a hybrid sea-flatwater kayak. The boat was fiberglass, about 11'10" long, and beamy (3').
When fishing on Sydney harbor I was mainly targetting small (up to 6 lb ) bluefish and some local fish known as flatheads (picture a northern pike who's head's been stepped on...same attitude, just better suited for hiding in the sand and exploding on passing prey). I didn't have any fancy gear, or even basic gear...not even a rod holder. I caught a lot of fish, and it was fun to get towed around by the bluefish and the bigger flathead. A net or something for handling toothy fish is a very good idea...I used to just swing the bluefish aboard, drop them in the bottom, and then try to keep their snapping, tooth-filled jaws away from sensitive areas. What can I say...I was young, I was foolish.
One good thing to have, especially if you tie into bigger fish like stripers (as I did on Montezuma) or wipers, would be a leash for your paddle. It is not a good feeling to have your boat going one way and your paddle going the other way. Rod holders are a good thing, especially if you have two sets. One set would be mounted for transporting rods (have they lie flush along the deck) and the other would be for trolling (I'd mount it directly behind you). You can definitely get going at a good trolling speed, even for fast swimmers like bluefish.
The biggest disadvantage with the kayak (compared to a pontoon or a float tube) is the tradeoff in maneuverability. Yes, they are faster and yes, there were days when I was able to zip over to a bluefish blitz or a striper boil and get my clock cleaned, but as soon as you put the paddle down to start fishing, you're at the mercy of the wind and currents. With a pontoon or a float tube you can at least drop your fins in the water and hold position. When working along a shoreline for bass, it can be quite a pain to keep putting the rod down, sculling with the paddle a bit, then picking the rod up, fishing one cast, then putting the rod down...you get the idea.
I would still use my kayak (if it weren't in storage in CA) because there are some lakes and situations where a pontoon or float tube just won't cut it. If you want to cover a lot of distance (4 - 5 miles) on a lake in one day, the kayak is the way to go. It is also a lot easier to deal with windy weather, bigger boats, and faster trolling speeds. For close-in, detail work, I'd go with the pontoon.
