You can build villages which will be friendly to you and you can destroy hostile ones in Minecraft. What's different about that and destroying civilizations on Spore?
Well for one thing, only areas around the player are active chunks in minecraft. So it doesn't matter where you build or who you meet because if you're not in close proximity with it, they're essentially in stasis.
Want to bugger off and let stuff cook in the furnace? Won't happen. Want to take a trip and come back to a chest full of eggs? Doesn't work.
You think the Pigmen will forget about the fact they're pissed with you when you re-enter the nether after a long absence? Nope, they're still out for blood.
Compare this to a game like spore or another 4X where colonies will produce or gather materials while you're away.
Further there is no such thing as a "hostile" village in Minecraft. Villages are neutral. They will defend themselves if you attack them, but they don't send out parties to trash your stuff or attack towns you've built.
Mobs will, but mobs can never be taken out. They will always always spawn. You can build a house with iron doors and the mobs will spawn inside because you left the light off. That's like a ship spawning out of nothing inside your territory. Even in Civilization, barbarians spawn away from your cities. Even then mobs don't attack your stuff (except villagers), they just attack you and any damage to your "colony" or castle is incidental to an attack against you.
Spore has several phases, all of which are obviously aping on other games. Some of the phases are adventure phases, then you get RTS battles, then you get space 4X. The main difference is that you have a hero rather than being some invisible, undying being
