RTS as in real time strategy, right?
Real time strategy games can occur in any setting. There are plenty of Space Age ones (Starcraft, etc.) and Medieval ones (Age of Empires). For a Jazz themed one, I'd imagine you'd have most of the action take place on the surface of the various planets and times that he visited throughout the Jazz 1 and 2 games. I'd imagine you'd be able to base your units off ingame characters and enemies. You could possibly have several "hero" units, based off Jazz, Spaz, Devan, and several bosses, like Bolly and the Queen or something. Most of your generic, "grunt" units would probably be turtles and rabbits of various shapes and sizes, with maybe some lizards thrown in.

I'd suggest figuring out how to get the game working before you try to build a specific setting or gameplay objectives. Once you know you can build bases, units, upgrades, etc and give commands to them, then start worrying about the visuals and gameplay specifics. Getting over that first design step is huge and challenging, and trying to do art and story and stuff at the same times will just be overwhelming.

Remember, making a game is an enormous project, and even a simple game can take huge amounts of time to make well. I've started several projects like this, only to realize how difficult it was and realizing I don't have that kind of commitment. It sounds like a really cool idea, and I hope you're more persistent than me. Good luck.