pretty clear there's a few ways to come at this problem and, not surprising, clear too that you're talking here, to the converted.
i've got a small sit in kayak. have had it since this Christmas. II love it! Most people go sit-on but I want to fish through winter, nights in winter, actually. Sit-in is decidedly the warmer way to go. My boat's paddle powered too - I don;t mind that at all.
So far, i've been exploring the Hawkesbury. mostly the quieter, often very, very small bits of water. A little boat is good for this. But, when conditions aren't too rough (wind and chop seem to be the big issue) getting out into Broken Bay has been fine.
There's is a lot of info already out there in the intereweb. So, just a few things I didn't hear mentioned before I bought:
Paddling gets you wet. I'm happy paddling, I kinda like it actually. But, I guess one of the really nice things about a Hobies and other peddle boats must be not throwing water up in to the air as you move around. If the wind's blowing the wrong way, you can get pretty damp on a long paddle. It is possible to be careful and not throw too much water around but if you like to paddle any distance, water is hard to avoid.
You can read a lot online about how comfy seats are. I would say, if possible, a few seating options is a great thing. I sit in and out (as in on top of the boat, feet on the seat) of the cockpit of my boat, and I have a foam pad that raises the seat that I can also put on top of the boat as well . Gives me a range of different sits. I've yet to feel I needed to go ashore for a break from sitting. A good percent of the people I have talked to tell me that after a few hours they tend to go ashore for a bit of a break. When you try out boats, sit in, on and all around them, try crossing you legs, etc, etc...
also really good is the option to stand up. In fact, it's a really, really, really good thing. Standing-casting is much nicer than sitting-casting. Especially if you're doing it all day. Some fishing - things like sandflats and working topwater lures - are massively improved by a decent view. I would add, I don't think your boat has to be super stable for this. Of course, this depends a lot on your balance, etc. I've fallen out once already. In summer, this was not a problem, as the weather cools, I'm being a bit more circumspect about choppy conditions and standing up! You really need to try a boat on the water to know how you're going to feel standing in it. Even then, you won't know exactly. My yak felt tippy when I first started standing in it, now, in calmer conditions, it's become very a comfortable, second-nature thing to do.
Stability is good BUT so too is how well your boat travels. If you incline to exercise and/or exploring, I will bet you come up against the problem of how far, with how much effort, your boat will travel in how long. I don't fully understand it but, I think, kayaks have a kind of optimal cruising speed - easy to get your boat up to that speed but going beyond that requires exponentially more and more effort. It's like a speed cap. Short boats are slower, wide boats are slower, stable boats are wider ...... speed comes at the expense of stability but you want both. if you can, test paddle some boats and when you do, push them, paddle hard for a few minutes to find out just how much they resist.
Following on from the above: if go for a paddle-powered boat and you don't mind exercise, a quality paddle is a very worthwhile investment. After an hour, the good behavior of a quality paddle adds up in to something very substantial.
I think, also, if you're new to paddling, a paddle that allows both length and offset adjustments is the best way to go. The odds of getting a right size paddle, with optimum offset when you've never paddled before are slim. There's considerable interplay between how you paddle, offset and length. I've been experimenting since I got my boat - at least once a week for the last 4 months and I'm still figuring out a best combination for general paddling. On top of that, I find, in any one outing, I vary the length of my paddle by 4-5cms and the offset by 10-15deg, depending on how I'm sitting, weather, etc.....
this probably is of little relevance but, if you're considering a sit in kayak, I think the cockpit size matters hugely.
cockpit sizes differ plenty. The cockpit in my yak is extra large and so it works nicely for gear, rods, & me etc..... I think a small cockpit could be very awkward. I do wonder if the general preference for sit on comes as much from cockpit size