I agree, I also likes the first part the most. But it wasn't that amazing either, it was just barely good as opposed to the rest of the game.

1st part: Cell - on the level of free Kongregate/Newsgrounds flash games, except with better graphics. Later an online game agar.io came out which I find better in regards to challenge, fun, replayability.

2nd part: Evolution - Very basic MMORPG, except single-player (the mmo part is being able to see other creations in your world). Animal creation was quite innovative, but also underwhelming, because it didn't affect the physics of the animal… Something like QWOP would be nice, where the computer would try to automatically convert simple controls to animal muscles…

3rd part: Tribe - Again, a simple flash game, boring

4th part: Civilization - again a simple game, I think the most challenging phase and quite fun, but building designing being only decorative was again underwhelming…

5th part: Cosmos - it had a Star Control feel to me, except it was simpler, and Star Control is a much older game!