In my opinion, if getting into the kayak in waist deep water is really the most important of the criteria that you listed above, then I think that you can rule out many, many kayaks. It is very tough to get into a yak in waist deep water if the yak is not either a sit on top or a yak with a huge cockpit (i.e. Pungo). Even then it is no small feat - especially in waders. Granted, you could devise a stabilizer system with PVC pipes and such. However, the Zen master in me is drawn to a simpler approach. With regards to the sit on tops: I do not like the idea. Remember when I was on Monomoy with you in July - even in the 80 degree + noon hour heat I was shivering. Sure, the exposure of your core body mass to a much larger mass of heat sinking, moving water is a recipe for core body temperature loss. Given. But on a drizzly dawn in September you will be in for a cold and bitterly miserable trip if you go out for an extended paddle in the rain. You could wear rain gear (kayaking and waders do not mix if you ask me) and get by but then again the yak experience is getting more complicated. Life is getting more complicated. You will be going nuts when I paddle off on a rainy day (in my yak with a nice neoprene spray skirt) and call you with tales of 40 inch cows jumping into my stripping basket! All with you on shore swearing at your wet and wild sit on top. Wait, you would probably be scoring your own 40 inch fish so maybe you would just be laughing at me for having to paddle so far in order to accomplish the feat...ignore this possibility.
So, in my opinion, forego the sit on top for the reasons cited above. You need a boat with a big cockpit and the Pungo is the place to start. The dimensions on the cockpit on the Pungo (L=55.5" and W=19") are far larger than the Manteo (L=29.75" and W=17"). Test drive the Pungo and see what you think. If you need to get into it in waist deep water then get out the PVC!
Just my thoughts - from a guy who has tried to get into his whitewater kayak (very, very small cockpit) in 2 feet of water with good chop and struggled miserably.