Can you tell us a little about the type of fishing you intend to do? Lakes, rivers, inshore, offshore, etc?
I'm a big fan of the Hobie pro angler series, it is a bass fishing machine. I've used it mainly in lakes and some inshore fishing for striper/flounder. I always prefer to stand when fishing since I rarely use live bait and am always casting, I've never been concerned with stability. I've always wanted to take it offshore but the thought of having to paddle that monster of a kayak 5 miles in a SHTF scenario (mirage drive failing) prevents me from doing anything crazy far.
I'm with you on the trailer being a pain, I always toss it in the back of my truck but I wouldn't worry about length if you have an extender. Just realize you will eat a considerable amount of bed space. This past weekend I traveled with a Hobie PA12 in the back of my Colorado (5'2" bed) with an extender, zero issues during the 3 hour drive.
If you are mostly doing lake/river fishing the Pro Angler is superior IMO. It's built like a tank and super stable, but you pay for that in weight (+120lbs fully rigged). If you mostly intend to fish inshore or offshore, check out the Outback or Revo series. I've had no experience with other peddle drives other than Hobie.