I have read a lot of science blogs complaining about how unscientific Spore is. As soon as I saw the creature creator I knew this would be the case... but it's true that the game is ridiculously unscientific from an evolutionary standpoint. This wouldn't be a big deal if they didn't go out of their way to market as and educational tool.. but they do. I have just two simple suggestions they could have used to make it much better.
Tech Tree! While it is fun for the creature creator to be able to do anything with all the parts, in the game, you should be limited to a tech tree where you choose paths to go down. This would also prove much more evolution like. You can't use the huge three prong claws until you have the small claws first.
Small changes. The evolve step should perhaps limit you more in terms of drastic changes. As the game is now, you can literally change the entire creature at any time. This change would make it more challenging to get what you want and more rewarding when you do.
All in all, I'm glad I never bought the game. The few hours of tinkering with it were enough. Nice graphics and creator mechanics, but that was about it.