(Hopefully not explaining something you already know!)
Since you have what looks like a 1:1 isometric projection, you can change the movement mapping from:
Up: (0, 1) => (1, 1)
Right: (1, 0) => (1, -1)
Down: (0, -1) => (-1, -1)
Left: (-1, 0) => (-1, 1)
Or something similar. Note that the vectors above are not unit length, so you might need to change it to something like UP: (sqrt(0.5), sqrt(0.5)) if you're multiplying by some speed.
Otherwise I don't think it was a bad idea to use isometric, it makes the art much more interesting to look at than a plain projection :D I do agree it takes more effort to work in though... Still, great job! There are a ton of great features for the amount of time you had.