Canoe is the way to go. Faster than jon boats and rowboats with the same motor, much more versatile and functional than kayaks. $20k less than a bass boat.
Stability really isn't much of an issue. Even in the downright stupid conditions I've gotten caught in with mine it held up OK. The large lake I fish most of the time gets very choppy mid-day with all the speed boats and cruise ships. But as long as the wind is <8mph I am usually good to go. Wind 7-8mph can make traveling into the wind a little bouncy. Fishing standing up is usually easy, the times it is tricky is with another person on board because movements are less predictable.
As far as propulsion, the 55lb thrust minn kota tm I have seems ideal on my 14.5' Old Town Guide. I had the 30 lb for a few years and it was fine, but the 55 is a noticeable difference in terms of torquey acceleration and battery life. Ironically I think the 30 got about the same cruising speed as my 55, ~3.5-4.0 mph, but I can get around 20mi from one group 27 battery with the 55, more like 15mi for the 30.
If you plan on using a motor then put some real thought/time into the mount. Especially for the 55lb thrust motor because its magnet is much heavier than the 30 and it will put a lot of stress on the mount. What you want boils down to one word: overbuilt. I wouldn't trus commercially made mounts personally. Mine is a beefed up version of this basic design ( http://oi65.tinypic.com/2u9oo3o.jpg ) using 1" thick oak boards, 1/2" dia carriage bolts and stronger L-braces.
I didn't find the battery box very useful. On my MK Power Center the battery meter was never very accurate and it does take up some extra space. Aside from the circuit breakers I didn't see the point of it so I leave it home now that I have 2 batteries.
Some other things I have are the bullnose rudder and a tracking fin/skeg on the bottom to improve tracking. For better cruising efficiency I got a kipawa weedless prop with larger angle propeller, but it's hard to tell the difference. Also worth getting are portable bow/stern navigation lights for nights/early mornings or if you just get stranded after dark.
Next plans are for a fish finder mount and a tool/lure caddy that can attach to the canoe yoke.