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.

http://sporedum.net/2008/11/05/will-wright-on-science-vs-cut...