Because the player’s microbe is steered by a 21st-century ape, it exhibits directed behavior atypical for microbes. The player can see nutrient patches and navigate toward them, while a real microbe would just bumble around and incidentally encounter nutrients.
Maybe the player should have to evolve methods of perception to be allowed to see things beyond the cell membrane of his microbe. In other words, I want the information available to the player to be limited like it is for microbes. Maybe the screen could be black at first, with only the player in the center. The player would move around aimlessly and incidentally encounter something to metabolize. The player would then stay in that area and continue to metabolize whatever it is. Eventually, the player would develop methods of sensing the world, and there might be blobby colored patches on the black background to indicate nutrients or heat or light or something. That way the player would evolve his organism to match its environment, just as real organisms evolve. A real microbe wouldn’t know what organelles will be useful in a few billion years; it just keeps doing what it does, either living or dying.