I've only paddled a small portion, but I'm intrigued by the Choctawhatchee. It runs from southern Alabama down into Florida and out into the Gulf. The upper reaches are pretty remote. Of particular interest is that people claim to have seen Ivory bill woodpeckers along it! No proof, of course, but an intriguing possibility considering the bird is thought to have gone extinct 70+ years ago.
Sounds like you're down my way... I'm in Jacksonville. What group are you planning trips for?