The multiverse can be used to tell stories in different ways than the main game. In this way you would have the arenas or station building that some people like.

One idea I just had was a young man wanting to get ahead starts smuggling items. Bribing guards that catch him (or other ways that will not attract too much attention).
After awhile he builds a base in an asteroid belt and deals with anyone who would compromise his base. He slowly builds up his empire even having contacts in the capital allowing him to move more freely.

Not sure the ending but this was an idea on how the black market started and having gameplay that involved avoiding conflict through bribes and influencing your enemies (bribe bureaucrats to lower police budget to get fewer patrols for example). Maybe an ending could be two top corp cruisers are sent after you for being too big. Of course most standard items would be removed.

any ideas for the multiverse that would provide more story or provide alternate gameplay?

I like that idea. Particularly making multiverse mods that exist within the same storyline (not sure if it would still be considered multiverse then). It also makes reusing assets make more sense (ie. the Ranx will still be the Ranx).

Personally i would like to make a mod about a gladiator and his fights in the arena :) Just might do it as well ^^