I completely understand how hard it is to make isometric movement feel less awkward! To answer your question on contrast, you could utilize complementary colors or play with saturation to have the text stand out and be more readable to the player while in gameplay. For the menu/movement instructions, you could up the contrast here have a dark multiply/overlay layer over gameplay, thus ensuring that the buttons can pop in comparison to the rest of the screen. Hopefully this clarifies a bit on my thoughts!