Dynamically changing color is thankfully an obstacle I have already overcome in ogre as you can see with the flashing organelles that take damage and differently colored membranes.
I think we shouldnt worry about organelles upgrades yet and focus mostly on bacteria models since moopli already has a prototype. If threecubed would like to create the models and Nanu texture them, that'd be pretty dope, but only if you both want to do that.
As for photosynthesis, a popular theory is that life started out with a purple algae that absorbed all of the suns yellow and green light. This algae covered all of the top of the ocean, and only red and blue light, which wasn't absorbed by the algae, managed to get through. In the, plants evolved that could use this red light (these are the green plants we see everywhere today). Unfortunately, the purple algae went extinct for some unknown reason and the green ones dominated.