I've decided to give Blender another go, since I never realised that Milkshape wasn't free. So I'm using This series (Thanks to Aph3x for the link) to try and get a grasp of things, and it seems to be going reasonably well so far.

I want to get to the stage that I can export a textured basic building in more or less any format (MD2 is preferable since I already have loading code for it), and get that into my engine. Then I can start doing some actual game stuff instead of engine nonsense, which should be much more productive, since I can see how the engine performs in real world situations.
My plan is to create a fairly basic RTS, like one of the Command And Conquer series of games, with a few single player missions (scripted with the script system), and multiplayer support (With the network system).

The engine itself is pretty functional as it is, the basic code is in, I just need to iron out some wrinkles with it.