Multi as in multiplayer? Absolutely will be top of the Todo list.
I like the library idea, but it also makes me wonder what kind of automation could be added? For example a system of nodes that can build itself? Then make it fight against the enemy in an arena like you said!
A story mode? Perhaps some travellers lost in space? Any suggestions on that?
I like the idea of scavenging too, that could be very interesting. For example there could be abandoned bases on the outskirts of the map that you have to build your way over to, take out the defenses that are still running on the backup power supply, and then steal then reroute all their resources into your base. This could include blue prints / materials for structures that cannot be built by default.
Another player made a fantastic suggestion that you could connect your nodes to enemy bases directly and pull resources from them. This mechanic would play perfectly into your suggestion here!
What do you mean about bosses? Keep the ideas coming, this is very exciting!