Well, what I think a good development plan Spore could've followed would be developing one stage at a time, and releasing them as they're completed. Like for instance, you could spend a few years on the Creature Stage and then release it and have all of your fun experimenting with different bodyplans and see which one is better, as well as eating up everything you see. Then after that is released, you work on the Tribal Stage, where you are intelligent, nomadic species that builds temporary structures and move to new places when resources run out, but when you find a comfortable spot like a river to settle along, where food is plentiful enough to feed a certain number of individuals, and when the population booms, half are willing to farm the food, while the other half is free to do whatever they want, thus effectively starting civilization. But for the sake of the development plan, you will just be a very advanced tribe. I'll need more time to think about what would be in the Civilization and Space Stage.
But even if "stages" are developed separately, I say screw stages, because then that'll tempt you to simply glue together separate games, and give them very rudimentary transitions (I mean, there is barely any transition between the Tribal and Civilization Stages, it's like they learn how to use electricity overnight).