These three options are very interesting, as we already said before.
Option 1 could be interesting, in my idea in seasonal way (maybe introducing some randomized climate change, simulating various geological eras), because day/night would be very confusing about time of evolution: my cell change in a week? That could give wrong information to the player.
Option 2 could be great: it’s correct and gives more depth in terms of gameplay. I absolutely agree to gives light an absolute value instead of percentage and to put a soft cap in terms of efficiency: the more photosynthetic organels you have, the less they are efficient.
Option 3 would make the photosynthetic gameplay much more complicated, i don’t know if it would still remains funny. I think that giving the player the chance to choose among all the possible colors of pigmentation could be too much. Maybe putting different organels could be better, in this way the player could be more strategical in the implementation of photosynthesis than now, where you simply run through patches to reach 100% lux and then spam out thylakoids. Giving the chance to choose the different wave length to absorb could be interesting if it doesn’t become frustrating.
Maybe could be a good idea to give a discount on the evolution costs when you change photosynthetic organels, otherwise when you change patch you could find a lot of your organels useless.