I'm not exactly sure how difficult this would be to implement, but one idea I had for when you go into the organism editor in aware mode would be an option to set the amount of in-game time between when you enter the editor and when you leave. The longer you set this, the more mutation points you'll get, but the auto evolution and population dynamics for other species will also go on for the same amount of time. As your species grows more and more intelligent, the maximum amount of time grows shorter, until by the beginning of awakening, it's large enough to create a new ethnicity but too small to make any dramatic changes such as a new species. Does this sound like a feasible idea?
One concern I have with this is that mutation always happens in small steps.
So for example with the development of the eye each time it becomes a bit more developed it needs to become more useful. So is it better to have some light sensing cells rather than none? Yes. Is it better if they are in a cup so you can tell direction more easily? Yes. Is it better if the cup is glazed over to protect them? Yes. is it better if the brain has more power to process the incoming signals? Yes. (Though of course this is all based on circumstances).
So letting the player have a tonne of MP in one go means they can just make some huge evolutionary leap which is unrealistic.
For example it would probably help if our brains were in our chests (because then they would be better protected). However it's not better for them to be in our necks, or to have no neck. So a smooth path doesn't really exist to move your brain from your head to your chest. It developed to be close to our senses and once that's happened it's hard to move it.
I think in the game it's important that there is a "creative mode" where you can just do anything you like. I also think that giving people as many MP as they want is going to be unrealistic. But that's just what I think.