I think it already helps, if the camera is not in perfect 45° but 40° angle, so the player can figure it out, if he needs to, but you keep that isometric feel. Also you could have the floortiles become brighter, the higher up they are to make depth perception easier. One last notch i recommend is syncing the particle effects with the beat of the music. All in all the game has a good foundation of ideas and i enjoyed it a lot, well done :)