Isometric games are possibly the HARDEST kind of 2D game to make. Period.
I would highly recommend starting with something a little easier, or perhaps using a pseudo isometric view (like in Legend of Zelda) where it's really top-down, but not... if you catch my drift. Even then, you will have LOTS of fun making sprites for it, as they will need at least 16 directions so they don't look badly animated... but preferably more.
I would recommend using a 3D application, like 3D Studio, Blender, ZBrush, or similar to make your sprites... that way you can make any angle easily.
The other way you could attack the problem is by making it more of a turn based game like Civilization... that way you could easily get away with more "iconic" style vehicles/troops/etc.