I wonder if part of the problem with spore is that it tried to do too many things at once. I've gotten the impression that while it is a fun game, none of the stages have a lot of depth.
It seemed like Sid wanted to focus on the experience of building a civilization from the ground up. But because of the fact that the game got watered down technically, early stages did not drastically alter future gameplay.
the thing with spore is, based on my understanding, is that the game that was initially designed and created got scrapped around alpha/beta. it was originally going to be much more in-depth science-like game, and worked like this in earlier versions.
then, some other people came in to help get the game produced and completed, there was an internal power struggle, and instead it got hijacked, re-done, cartoonified and scaled back in the name of making it marketable and to finish it on time.
My understanding is that the main "cute" vs. "science" design issue in Spore was whether the character animation/simulation system would directly influence the performance of the creatures. Early on, presumably, creature performance was directly driven by the simulator, and some of the staff liked the challenge of trying to find the creatures that performed best in the simulator.
There are a number of problems with this gameplay dynamic, however. The big one is that with a complex simulation you have little control over the performance maximas and minimas. What if, for example, the simulator decides butterfly wings are a universal detriment? At that point, you might as well remove them from the game, since no one is going to use them. What if the simulator decides that there is a "best" creature design, and that it is a three-mandibled octopod? That will become the design that most players use.
You really don't want a "best" creature. What you want, ideally, is a rock-paper-scissors stalemate, so that players try out multiple designs, each of which has advantages and disadvantages. This is hard to engineer with a simulator. So, instead of using the simulator directly, they built a separate creature interaction model that they had more control over.
I think this was the right decision and that choosing the alternative would not have significantly improved the game.
It seemed like Sid wanted to focus on the experience of building a civilization from the ground up. But because of the fact that the game got watered down technically, early stages did not drastically alter future gameplay.