Here's a note I sent to a fellow BR member who had a similar question..........
The important thing to understand with kayaks in general is that not all of the hulls have the same functionality or purpose. Some hulls are wide for stability but can be a bear to paddle. Some hulls are very narrow and fast but are a little less stable and not always easy to stand in. The key is to find a balance of both attributes while still being able to enjoy your time on the water. Your question about seats is kind of a loaded question, because up until the last year, most factory kayak seats left a lot to be desired. The only line of kayaks under the $1000 price point with a comfortable seat was the Native Ultimate and Manta Rays. While most kayak seats are fine for a 2 hour outing, anything longer than that would require frequent stops to stretch your legs and your back. Some factory seat positions and footwell layouts are so difficult to get comfortable in that your legs or feet fall asleep. A perfect example of that would be the Perception Pescador or Native Redfish where your legs and seat are basically flat. You can always spend the extra cash and upgrade your seating to an upscale model like the Surf To Summit GTS Expedition, etc. but that involves and additional $125-200 outlay depending upon whay you opt for.
With that said, the last year has seen a significant focus by the industry as a whole on improving the kayak seating features on the various brands of kayaks out there. The models that come to mind are: Jackson (Coosa & Cuda), Wilderness Systems (Commander series, plus the new Air Ride seat they offer for their Ride line), Native Watercraft (Ultimate, Slayer and Manta Ray) and the high end Hobie Pro Angler series with the new Vantage seating. All of these are good choices from a seating perspective, but they each differ in their overall stability, handling and tracking characteristics.
As far as the hull designs, the hulls with pontoon style hulls tend to be more stable than others, but new models like the Ride series have design characteristics like deeper chines that provide a good level of stability. Now, as far as kayak types - SOT, SINK and the other types you may not be aware of are the hybrid and alternative propulsion models. SOTs or Sit On Tops provide a great level of safety, because they are designed to drain any water that enters the kayak via the integrated scupper holes. SINKs or Sit INside Kayaks do not have any form of integrated scuppers or drainage capabilities save for turning them over or manually via a small hand operated bilge (common accessory that several of my friends carry with them, so don't let that scare you). The hybrids are an interesting choice, becaase they offer the stability of pontoon style hulls with a seating position similar to a canoe, but still provide good tracking and speed characterisitics (Native Ultimate & Tegris models or Wilderness Systems Commanders). The other option is a hull that has alternative propulsion methods. This can be either via manual propulsion (Native Mariner or Hobie Mirage drive kayaks) or powered (Ocean Kayak Torque, Native Propel or adding a powered solution from Torqueedo or Bass Yaks designed for a specific hull - most common one is the Wilderness Commander).
If you are going to be loading the kayak manually on top of your vehicle, then weight is a concern and hulls that weigh over 70 lbs. may be a challenge unless you opted for a load assist bar from Yakima, Thule Hullavator or the new T-Bar system from Rhino Racks. If you opt for one of these systems, then kayak weight is no that much of a concern. I know my next vehicle will most likely have the Rhino Rack system, so I can then purchase a Hobie Pro Angler 12 or 14.
Regarding rod storage/carrying capabilities - rods can be carried in a number of ways: via crate assembly with an integrated 3 rod holder (what I use right now), via rod holders installed behind the seat (most kayaks can accommodate 2-4 angled rod holders - a friend of mine actually has 3 on each side for a total of 6 plus a 3 rod holder on his crate pack, the other option is via rod holders that are attached above the hull (typically RAM, Scotty or Cannon mounts). Your ability to carry rods is only limited by what you are willing to do to accommodate your needs. Just remember - the more rods you carry, the more chances of getting tangled up or possibly spending too much time switching rods versus dialing in on the fish. A common mistake in tournaments from watching other kayak anglers. The one exception to these statements is for two specific models of kayaks - the Jackson Cuda or Coosa and the Hobie Pro Angler series. The Jackson models have what they call rod stagers that basically place the rod butts a top a bungee under the hi/lo seating and stage the rod tips in small molded cutouts in front of the footwell. The Hobie Pro Anglers have integrated rod tubes that can accommodate up to 6 rods (including fly rods) on the PA14 and up to 4 rods (including fly rods) on the PA12.
You mentioned that you would like to stand - the ability to stand and sight fish at certain times of the year would be a key variable to consider - that would lend my recommendation to one of the following models: Native Watercraft Ultimate 12 or 14.5 & Slayer 12 or 14, Jackson Cuda 12 or 14, Wilderness Commander 120/140, Ride 135 or the Hobie Pro Anglers. With the Native, Jackson or Wilderness models, you could contact BassYaks and order the specific powered motor option you desire. The Pro Angler you would use your legs to power the PA and leave your hands free to fish (very advantageous in current and wind). As an individual that has shoulder problems and a less than perfect back, I love my Hobie Revolution 13 and one of the reasons I am proud to represent them as the Local Pro Staffer in Central VA. Just remember that the addition of any powered form of propulsion will most likely require registration per your respective state's requirements.
As far as storage capabilities, the hybrids and the Pro Angler offer the most flexibility to carry a cooler and additional gear. With that said, there are several custom DIY mods that folks have done to blend these needs. A common one I see is using the medium ractangular Coleman coolers and attaching a 3-4 rod holder on the back or sides using s/s hardware and then using small tackle bags or binders for their other gear. Most rear tankwells have a bungee system of some form that will permit securing items to some extent. For me personally, I have two crate systems both involve using the Coleman Snack Mate personal cooler (hold a lunch, snacks and a few bottles of water but small enough to stow up front in my bow hatch or in the tankwell behind my seat). I also have a soft sided Hobie cooler that I stow the same way. My two setups are: a standard milk crate with a 3-rod holder attached via the Precision Pak crate mate sleeve, and then I have a Flambeau medium sized marine case to store my tackle trays inside and just carry my rods in the integrated rod holders on my Revolution 13 and in the rod holders I attach up front using YakAttack GearTracs. Here's my fishing vessel of choice right now.....
https://lh3.googleusercontent.com/-50Q1_6Ell5Q/UAygshIQVHI/AAAAAAAACK8/5VgT9Ia0RFQ/s1024/P7220017.JPG
https://lh3.googleusercontent.com/-ti4KrNp0VG0/T5VCR6KiUrI/AAAAAAAABwA/Q65o73c1NMA/s1024/SAM_1428.JPG
https://lh6.googleusercontent.com/-S4MzazrlPOk/UFzYauwfo6I/AAAAAAAACns/2pE4TAnxEjg/s1024/P9210003.JPG
I hope this helped answer some of your questions.
Chuck