A nice way to go with your prototyping is to make a small, playable game (for yourself or not) that uses a few of the core systems you want. Individual systems are great, but the combination can sometimes be the tricky part. For instance, you could work on your pathfinding, layout abilities (try things like elevation, proper z-ordering, etc), and in-game events by making something simple like leading a group of units through to specific points and having something happen when you reach them. A few small things like that will give you complete ideas on where you want to go with it all, it would teach you everything you need, and you would be able to follow through with completing more bite-sized chunks of stuff. You could do a personal example strictly based on UI-handling and number management. Prototype your battles with just single units vs single units, then groups, squads, armies to make it all more manageable. Those three demos/prototypes for yourself wouldn't take incredibly long to achieve, but you would be FAR ahead of the curve in a couple months when you could start cranking on the real deal. It's much harder learning each of those individual things along the way.
Soon after those are done, and probably while you're working on implementing everything (quickly now!) into the main game, do some concept art tests to make sure your development art will line up with how you want the game to finally look. It would stink to get everything nailed down then add in art only to find it all looks wonky. Just do a bit of graphical planning alongside your systems implementations so you don't have to rework things again later.
And lastly, don't forget audio! You don't have to make it all until later, but you should have an idea in your mind about how you want to implement it all. IE, decide what cues what and possibly set up your functions sooner rather than later so you really can just plop in the audio files and be ready to go with some mixing.
It sounds like you're going about it logically, I'm just encouraging making sure your prototypes are truly useful creations that can possibly kill a few birds with that one stone. If it all sounds like a lot, though, it's because it is.