The thing that hurts my brain is just the way the movement works. The controls are technically on cardinal directions but because of the isometric view it looks like it's in a intercardinal direction, so it becomes confusing what direction I'm moving in because I don't have a clear frame of reference what's up and what's left and so on.
The first thing that comes to mind would be mouse/cursor based movement. Either you click the tile you want to move to, or you could use arrows or maybe WASD to move a marker to where you want to move and then press a different button to move there. I would suggest looking at other isometric games and see how they handle movement to come up with your own ideas on how to tackle this problem. I believe they handle it in similar ways to what I've suggested, but actually seeing it for yourself would probably be better than me trying to explain it.
I hope this helps!