There are a number of such games out there, especially on Kongregate. It comes in various shapes, and most developers ended introducing minimal gameplay elements to the core aspect so that the player is bit more involved.

Ask yourself, how could the player interact with this in a fun way?

The core of your game doesn't have to change.

It appears to me like you're essentially working on a "God" game. Embrace that.

The thing that made it interesting/fun, was the conflict. You were watching the war of existence. If you implement pheromones to these creatures you'll find a whole new level of "fun" since you'll watch as they are attracted or reject the trails these creatures leave behind. Conflict is at the core of every game, and the challenge of creatively overcoming it. The driving factor of evolution is the pressure of scarcity. We work/fight/aim to win the hardest when the chips are down. If that means changing everything, we either do it, or we die. It's fun to watch someone win. In evolution, someone always wins. (feel free to use that;)

Hmm, just thinking, but imagine this :
There is a map/playing area/mad scientist's lab where the evolution happens, and multiple players have god/scientist/gamer-options to manipulate this environment;

in a challenging mode they would all try to develop a certain kind of creature(each a different one) while the environment only has enough living space to support only (maybe players minus one, maybe only one) creatures.

There could be a coöp-mode where 2 or so players both try to evolve some kind of creature, both of them are going for a different creature(some kind of challenge they both individually want to accomplish) and maybe they only succeed if they are succeeding both at the same time(make sure bad players won't be making the starting levels impossible to come through)

A free/sandbox mode is off course standard in such a game.