Last year I asked the same question.
We ended up getting the Pelican Apex100:
As has been previously pointed out: the kayak doesn't make a great tender i.e. not very useful for ferrying people, supplies (unless in small amounts), fuel etc.
We felt that the sit-on-top model would be easier to get in and out of - I think we were right.
On the plus side: the biggest mistake we made was only getting one. My wife and I both love to putter about in the kayak and can only go one at a time (my boat isn't big enough for a tandem.
I think of all of the toys we have got for the boat, the kayak is the most enjoyable.
I use it to explore. I take it ashore as well, but realize that I won't be dry when I get there.
I have a waterproof camera (video and still) and the kayak makes a great platform from which to sneak up on wildlife.
I find the kayak to be surprisingly stable in a bit of a chop. I prefer to paddle downwind, but it seems to track alright going into a moderate wind.
I don't think I would use the kayak for any serious trekking, but, for what we use it for, we are very satisfied.
I did spend some time at one anchorage trying to flip the kayak and get back onto it from the water. It was surprisingly resistant to flipping. Getting back on wasn't pretty, but it was relatively easy to do.