For fishing a sit on top is superior to a SIK for stability and layout. A SIK may be drier, however, you would usually be wearing waders in cooler weather anyway, so that should not be an issue. It is much easier to get into and out of a SOT.

As far as paddling upsteam, you should be able to paddle upstream with a kayak as well or better than in a canoe. Standing up is another issue. Its one of those situations in which you either can or you can't, depending on you size and balance. I can't do it on still water in a Prowler 15, while I know a lot of people who can stand in a less stable kayak in rough water. Pontoons can help you stand and fish, but they create a lot of drag and will slow you down to a crawl.

The three best fishing kayaks, IMHO, are the Prowler 13, Tarpon 140 and Heritage Redfisher 14. If you want more speed and better tracking, the choices would be the Prowler 15 and the Tarpon 160, but given your situation, I don't think the gain would be worth it.