There is one obvious omission from Spore: the 3D underwater phase, which, according to this interview, had been partly developed, but was cut.
I had wanted to take my cellular creations on a gradual path from the microscopic to the macroscopic in a 3D world filled with bizarre aquatic creatures.
However, instead, you go straight from a single cell to a vertebrate with legs, and find yourself somehow eating whole fruit with your filter-feeding tentacles.
I can forgive Maxis for leaving out 'water world,' but they could have incorporated a less abrupt system for the cell-to-land transition. Despite the heartwarming cut scene, it feels like it was cobbled together at the last minute.
Something as simple as requiring players to replace all of their cellular parts would have made for a better experience. For example, my first attempt at a land-based creature couldn't walk, because I had given it fins for feet.
My only clue as to what I had done wrong was the name of the fins: cilia. Real life cilia are like fuzz, so of course you couldn't walk on them. But because Spore let me keep my cilia as macroscopic structures (and they sure look like fins), I assumed my creature could still use them for locomotion. I was wrong.
On a more amusing note, another missing feature is procedural mating (they kept the dance, but not the finale). Apparently, the creatures of Spore have figured out how to produce hard-shelled eggs without internal fertilization - and good for them! Players are already going to spam the world with Sporn; there's no need for the game to offer them any encouragement.