While the AutoEvo system is super fun and is definitely a very good addiction to the game, I think the game would benefit from adding some pre-made cells, while also maintaining the randomly evolved ones: for example after your cell has reproduce a certain amount of times you add a fast and dangerous predatory cell, a completely Photosynthesis based cell that doesn’t move, a giant cell that moves slowly and engulfes everything on its path and many others, each maybe specific to a patch or a patch type. I am aware this is going to remove variety from the game but it will add consistant enemies and probably make the game more fun. You can also make it so the pre-made cells have some differences from each play through, like color or shape, and also make it so after they spawn they keep evolving with the autoevo.
I don’t think it’s a very good idea to remove one of the core concepts that the player is the LUCA on their planet. Also adding random species that have not evolved in the current environment may also immediately become extinct as they aren’t suitable for the competition situation they are placed in, or they might be super good and cause extinction of all the species that were already there.
i caused the extiction of all the microbes in my patch 
That isn’t possible. The player’s species would speciate and there would would be new species as good as the player’s cell.
That doesn’t happen immediately. There’s a random chance for the biodiversity increasing species to be created so it isn’t always guaranteed. Thus it is possible to be the only species in a patch for a couple of generations if you are lucky enough (or maybe unlucky).
Perhaps the AutoEvo system should encourage specialization in cell function. The current autoEvo system prefer adding cell structure to retrenching cell, that makes all cell very large and complex.
Well the problem with that is that some people are still complaining that auto-evo doesn’t make big enough prey / competitor cells for them. The second problem is that no one really wants to work on the auto-evo as it is very complex and difficult to balance it (see the first problem, you can’t please everyone).
since there are going to be mass extinctions i don’t think the player should be LUCA but the first organism as all life but one organism including the player could get wiped out by a mass extinction(possibly caused by the player even)
i forgot to include this earlier but there are also mods that make the player not even exist in a way that can interact with the environment
I cant comprehend your logic here
neither do i
When you havent logicked: