Eric,
For anyone who hasn't paddled throughout Florida, it contains a lot of unique ecosystems. You've got the everglades, the keys, mangrove lagoons, crystal clear spring-fed rivers, marsh grass, and pine habitats. For me, each ecosystem had its own treasures, and I want to go explore every one a little further.
I really enjoyed the everglades. I paddled along the gulf (gulf of mexico and florida bay) route, which is around 100 miles between resupply points. I never imagined the everglades being what I saw. Unspoiled beaches, white sand teeming with perfect shells, palm trees, and wildlife. I saw wild deer, alligators, crocodiles, tons of dolphins and sharks, osprey, and eagles. It was remote, and my teammate and I didn't see another person for almost five days, and then that was a solo kayaker. We had a nice breeze, which kept the bugs away. I'd like to do a loop paddle in the next year or two, paddling through the wilderness waterway (the interior everglades) and then looping back along the gulf. It would be around 225 miles.
The keys weren't nearly as remote, but if you are looking for crystal clear waters to paddle, fish, snorkel, dive, play... and have lodging and restaurant opportunities, that's a great place to go. You can paddle on either the atlantic or the florida bay side, offering a complete change in habitat. The Florida Bay has small mangrove islands, seagrass, and relatively calmer waters, while the atlantic, well, it's the atlantic, so there's more exposure and deeper water.
Along the Southwest coast, there's the Great Calusa Blueway, which is a collection of paddling trails that are well-marked, and offer a mix of camping options as well as lodging options. The people who have been working on the Blueway have done a great job at making a trail that is very paddler-friendly. You are almost guaranteed to see great game fish- redfish, and snook.
Hope that gives you a little info. I'm hiking now, on my way back to key west with Jodi, my partner, so computer time is not always available. So, if there's a delay between responses, that's why!
Thanks,
matt