It doesn't feel immediate to adjust the gameplay in this regard without making a whole different game, the story as it is works pretty well: you come onto an alien planet, plunder it, pollute it, kill all life, burn all trees, as you grow more powerful and more resource-hungry
![Twisted Evil :twisted:](./images/smilies/icon_twisted.gif)
But still, being able to play peacefully and cooperate with alien life would be tremendous.
One of my biggest wish for the game is that there are some incentives to build a complex transport network at a large scale. Right now, you do this, but only in your main base. There's no reason to manufacture anything out of your base.
One possible incentive would be to trade with aliens. But even better would be to use alien's 'buildings' to transform products. This way you can bring the transport network gameplay from transport tycoon games into Factorio!
Aliens would have some kind of buildings (probably slimy ones) to which you can bring some materials and get finished products / semi-finished (you'd probably have to pay them with some of your goods or theirs also.) You could have to transport goods amongst several alien bases to get the full chain.
The corresponding goods could intersect with existing chains or be completely independent.
Finally, if your cooperation with aliens is going great, you might be able to have some tame aliens who will build some kind of alien factory for you at your chosen location.
On the other hand, if you prefer to play the military way, you could wipe their base except for their factories, and power them yourself, so that you can access their manufacturing chains without cooperation. Or enslave some of them so they work for you in their factories.