I think the darkening would be best. The 3D aspect is a neat part, but I don't think you want too much height difference to where the player has to jump to move around. I like that the flagged blocks are raised, and if you raise the others, then you probably need to raise those to stay above. Perhaps the flagged blocks requiring jumping wouldn't be too bad, but moving between revealed and unrevealed should definitely stay at a level where you can freely run between them without jumping.