For ideas take a look at the Native Ultimate, it's a kayak/canoe hybrid that is very popular with the paddle fishing guys: http://www.nativewatercraft.com/ult_12.cfm
I have been thinking of something in that line as well, I sold my 15' canoe because it was like a barge, and my 14' fishing kayak feels a bit cramped - not enough room to move and storing stuff in hatches is a pain.