I recently had the idea of implementing the idea of having your organism evolve via traits you gain as you play. I had this idea while playing a game by Paradox Interactive, called Crusader Kings 2.
Above you see Vilfred I, duke of Livonia and Prince-Consort of Norway. The traits that Vilfred I has are, from right to left:
Envious, Proud, deceitful, brave, gregarious and falconer.
These traits build up the skills that Vilfred has, which are above the trait icons:
Book- Research tech
Aside from a ballin' mustache, Vilfred is useless in terms of gameplay. His skills aren't exactly the greatest, and certain traits cancel each other out, such as deceitful and gregarious.
The final trait icon Vilfred has is his career trait, when a child comes of age, all his traits are weighed in, giving them careers such as Misguided Warriors, or in Wilfred's case, Drunken Wastrels. All these perks determine the type of ruler the character will be.
Now let's merge this with Thrive.
Let us assume that our microbe and multicellular creatures both evolved primarily by relying on consuming plant matter. This would give the creature the base trait "Herbivore", which would only determine the diet.
Now let us say out creature grows a bit larger as an aquatic organism. In the specific biome it lives in, members of our creature's species that are more competitive and aggressive survive more. This would give our organism the trait "Aggressive-Orientation.
So far, we have a herbivore fish that is aggressive.
Now let's assume of angry little leaf-eating sardine crawl onto land, where it finds out that working in living in herds gives better chances at survival. This would now give our beast the perk "Pack Mentality".
So now we have aggressive herbivores roaming in packs. Let's assume that both traits "Aggressive-Orientation" and "Pack-Mentality" give bonus to combat skills. Now when travelling as pack the creatures do bonus damage.
Fast forward to the society stage. Our animals have taken the path of war, destroying any other tribes that have risen up. This would give our species the trait "Warrior", again giving the bonus to military.
Now at the nation portion, our creatures find out that the world is harder to conquer alone. They decide to form military alliances, along with trade routes. This would give them a trait along the lines of "Diplomat". Because Diplomat is a peaceful trait, it would reduce the effects of the combat skill previously given.
Now we move towards the beginning of space stage, where our society has conquered the world peacefully. The final trait they would gain would be something like "Peaceful", which would cancel out the perk "Aggressive", due to the conflicting nature.
The career trait would be determined through previous traits. However, I personally think a career trait would be unnecessary.
The perks I listed above were mainly personality based, however, ,physical attributes would play a part. Let's say we never crawled out of the water and instead swam into the open ocean. Now in order to survive we would need to gain the trait "Swimmer", allowing us to move faster in water. A good point to make is that as you evolve, you would be able to get higher levels in certain traits, such as "Swimmer +1" or "Highly Aggressive" as you use those skills to your advantage.
I also believe that the perk system would allow us to fill in food webs efficiently, seeing as predators and herbivores would be assigned early game, with higher end predators coming in with better perks.
Now the part I think would be interesting. Certain perks would augment the appearance. Let's say out species managed to conquer the ocean and gain "Swimmer +3". The bodies of our species would be much sleeker, which fins and tails being built more towards movement instead of grasping. Faster land creatures would be able to gain sleeker bodies as well, and more aggressive and combative creatures would begin to grow claws/horns.
Thoughts? I know it seems a little complex, but it would a way to combat problems with auto-evo.