One big issue I have discovered, and this depends on the geo/physical situation you will use the kayak in, and that is WEIGHT. I, too have been kayak fishing for quite a few years, since 1997, I think, and have watched the development of fishing kayaks. It has exploded recently, and you can see what has been successful by what is being repeated. Storage: It seems they find places everywhere for everything. That's nice because it uses space efficiently, hoping what is done doesn't get in the way. so make sure there aren't features that will interfere with what you are doing. And often, this doesn't make itself known until after many trips, unfortunately.
Size: 12 ft seems to be the sweet spot, and I have had 3 kayaks of that size. I wouldn't want anything smaller b/c 12 ft is small enough. I wouldn't want anything much bigger due to handling and lifting. Less is more here. I have a 16.5 ft. Native ultimate tandem that is tough to cartop but easier than a canoe that it replaces. But that's an extreme. it isn't heavy, it's ungainly.
Weight: related to size. The new fishing kayaks like the Wilderness Ride and Olde Towne Predator and Native Slayer are too, too heavy for me to use. It'd be OK if you used a drive-up launch or even had a trailer (add $1200 for that if you don't own one). I use my kayaks mostly on the Allegheny River. None and I mean NONE of my floats have 2 simple, direct accesses to the river. In fact, I'd doubt just about anyone else besides crazy me would do the one access that I do below Franklin. A too heavy boat would be prohibitive. If your waters have good accesses, great, BUT it will limit how or where you can access more challenging waters. If you can't hump it to or from the water in some way that very much depends on your ability to lift and move the kayak, then that water, your kayak and you will NOT meet happily. That's one reason I won't get a Ride or Preadator. There is a new Native ultimate coming out this year that is more comfortable to stand in. The Jackson Kilroy is a sit-in with higher sitting options and is lighter for its size than other sit on tops.
Standing: I have become a huge fan of standing in kayaks. It was the holy grail that I have pursued since I started kayak fishing. I solo paddle the 16.5 ft native tandem when I shouldn't when I want to stand in it. You can't flip and pitch while sitting down. Not well. this is your choice, but wow, its fueling my next purchase. I'm favoring a sit-in based on lighter weight, greater stability, variable height seating positions and glide and silence. The scupper holes make some noise and, with noise, drag.
Well, that's about it.
JB