About the space station...

I figure you do a mission but then you have to purchase the upgrade from someone on your space station.

Like you go on a quest "Find Gertrude the Barkeep". Then you go to a planet to recruit/rescue Gertrude. When the quest is done she'd wander you station but going "You know, I'd be more useful if I had a bar". And then you have to purchase the bar. However, since you had to go through a mission so you could purchase it the purchase wouldn't be especially expensive.

Alternatively you could purchase the bar and it would activate the quest to find Gertrude. I find this idea more believable though since the community would just find the first idea irritating in the long run.

 

I would say it should be a mixture. eg do a quest and some guy gives you a schematic ( or just find a schematic as treasure), collect resources to build it

BUT what is most important to me is flexibility. Make it in modular sections but let people stack and join them and decorate them how they want.
Part of the appeal of terriara was being able to build a house and make it just how you wanted (Used to love decorating houses in Ultima Online as well)

 

Gertrude