Speaking of passive evolution and endosymbiosis: it would be nice if you can have more unique organelles/endosymbionts other than just mitochondria and chloroplasts (by engulfing prokaryotes that specialises on other things than photosynthesis or respiration). Also; I think it’s better if you don’t spend MPs that will magically give you a chloroplast or mitochondrion, instead you should just “eat” a prokaryote that is a closest approximation to cyanobacterium or [I forgot the name/type of that bacteria] respectively. Then, to manage how many of them there are inside, you take care of how much resources they can get; like you’re managing a farm of these organelles. I think of these organelles like they’re citizens of a city called a eukaryote. That way, it’s (almost) free/easy to get an endosymbiont organelle; then you can place a given amount depending on how well you took care of them.
In real life, these organelles (mito/chloro) are their own separate living entities controlled/enslaved by the nucleus (in a way). So it’ll be nice to see them behave the same way in the game.
Edit: I want to add that the endosymbionts can still evolve inside your cell, and that they can come from parasites as well (if parasitism can be a potential feature in the future). I also want to give a shout-out to @hhyyrylainen for moving this post, thanks ( ◜‿◝ )