I know that random chances aren’t exactly the most ideal of approaches. However, while I’m not a game designer, I genuinely can’t think of a better way to deal with this problem within the planned framework of the game. Mutation points are the main limitation here - whilst they work great for simulating the small-scale, gradual changes that happen over eons, they’re inadequate at representing endosymbiosis. I mean, adding more mitochondria to the cell, or changing the potency of an agent, or increasing your heat resistance - all of these are gradual changes that can be well-represented by the MP system since they can actually be quantified. It’s impossible to quantify the emergence of photosynthesis/eukaryotes/chloroplasts against adding an additional cyotplasm hex, or whatever. They’re just too big of a change that doesn’t even follow the conventional route of evolution and emerge only under very special circumstances.
If the game sought to represent their importance and rarity compared to your average mutation, they would have to cost way more than 100MP, and such a thing would be impossible within the 100MP-max framework of the game. It would require some sort of mechanic wherein you could stockpile MP points, and this would not only be jarringly unrealistic, but would also almost defeat the whole purpose MP points had in the first place, which is to force evolutionary changes to be gradual and make sense.
And I think that a certain amount of weighted chance would work OK. If the chance of getting chloroplasts was literally just 5% every generation, yeah, that would suck. But say it starts out at a low chance, but is heavily modified by environmental variables and your actual playstyle, and perhaps even the chance gradually rises as time passes and if you fulfill certain criteria, that would be far more fair, IMO. It would still reward players that play appropriately, while weeding out cases where evolving them absolutely would not make sense (e.g. if you live 5000m below the surface and there aren’t any photosynthesisers around).
And so far as I know, the current plan is to make it random chance. As Omicron said, it’s planned that you have to eat the appropriate prokaryote until the dice-gods smile upon you and you get the organelle. Personally, I’m against forcing the player to actually have to eat these prokaryotes during play-time itself, as that would likely become very grindy, very quickly. But a check of the player’s diet at the end of every generation would suffice, IMO.