After reading through these posts the image I have in my head is like this: (Just gathering ideas, adding a few of my own)
You view the immediate environment around a 'nest' of your creatures (this could be as cells or more developed forms). You can see around them some environmental features; things that they need to survive and/or harness for a purpose. You have are able to place markers/waypoints (could be either generic or perhaps split up based on actions (eg collect, explore) or needs (eg hunger, thirst) that need to satisfied. I would rather specific guidance to make it more of a game rather then a sim) thus guiding your creatures actions, letting them evolve (as detailed in wallishs post). Each individual evolves on its own, rather then informally.
As your population increases (or perhaps as a result of exploration) the scope of your environment expands bringing with it more environmental elements (resources, other creatures). From time to time you will have to manage changes, like new predators, that you will have to evolve to accommodate in order to survive.
Perhaps once your population becomes quite expansive you will no longer be dealing with creatures but communities (no necessarily more advanced technologically, just large groups of your creatures). Evolution may be handled on a community basis, rather then individuals so that it can be managed easier processor-wise (talking out my arse?).
I also like the idea that your dudes will not only evolve on a biological level but a cultural and technological one. Given a change in environment some interesting interactions may arise. When you start out you are focused on biological evolution but as the game progresses cultural and then technological evolution is also important. Note that I am not using the word 'progress'. The idea is that tech evolution will flow from how they have culturally evolved which will flow from their biological evolution. In this way the game changes with a sense of progress and the player has new challenges. Of course this may be outside the desired scope.
Anyway, I think we need a seperate place to talk about this. That way we can split out the different discussions at hand so that things can be more organised and discussion will be more focused. (and people won't be ignored!)