If you're familiar with the game Civilization (I'm thinking specifically of Civ:Revolutions), Factorio's victory condition is similar to a "Science" victory there, where one launches a rocket into space.
My suggestion is that the game should have multiple victory conditions. Again, riffing on Civ:Rev, we might have...
* Science: Like now (Possibly: require every known technology to be researched)
* Military: Some sort of "total annihilation" or "overwhelming force" against the aliens (yes, I know it's an infinite world; the details would have to be TBD, of course.)
* Diplomatic: Some sort of peaceful treaty is reached with the aliens. (I saw the thread about peaceful co-existence in DevProposals; this idea is to develop that into a victory condition)
* Financial: We don't really use money in Factorio; perhaps this would be a "completely pwn the resources" victory. I don't really know what it might look like.
* Cultural: build a factory so beautiful and marvelous that the aliens actually want to be part of it. "TBD" -- again, I have no idea what this might look like.

I'm sure there are a handful of other ideas, but the point is to add variety to replays, rather than always trying to reach the exactly-one victory condition and perfect one's technique there.
Related but separate (another idea stolen from Civ and other games): the "fully configurable game parameters" thing is cool, and should remain as "custom settings", but it'd be nice if there were 4-6 "default" levels, say...
* Noob/Kindergarden (resources everywhere, limited numbers of weak bug spawners, slow evolution, etc.)
* Easy
* Normal
* Hard
* Epic
* Impossible
Or similar. Again, the idea being to add variety to Factorio replays without requiring the player to remember what custom settings they used on the configuration page.
Loving the game! I'm a relative noob -- came in at 1.12 (.22?) -- so missed the earlier revs, but those are my ideas.
Thanks!