Here is something that came to mind that you might be able to incorporate. White Holes. Never used in any game that I know of and not well known. Basically a reverse Black Hole. Thought it could be used for your cross universe ideas and you could limit usage by needing a top level skill to be able to navigate Black Holes and White Holes
Here is a partial quote from Wikipedia on the subject. Basically the same as a wormhole in a way, but a little more unique.
There are theories suggesting that white holes create new universes from matter originating in another universe's black hole.[8]
A more recently proposed view of black holes might be interpreted as shedding some light on the nature of classical white holes. Some researchers have proposed that when a black hole forms, a big bang occurs at the core, which creates a new universe that expands outside of the parent universe.[9][10] See also Fecund universes.
The initial feeding of matter from the parent universe's black hole and the expansion that follows in the new universe might be thought of as a cosmological type of white hole. Unlike traditional white holes, this type of white hole would not be localized in space in the new universe, and its horizon would have to be identified with the cosmological horizon.[citation needed]
Expanding a little more on this. If you read more on wiki. One theory suggests that both can exist simultaneously in both universes. This could provide a unique game experience. You could separate skills for both. Black holes will suck you in and destroy ships until black hole physics reaches a certain level. At that point It would transport your ships to the other universe. The same would be said for white holes. Initially destroying ships with tidal forces Then white holes could throw ships away. Throwing them across the same universe since it is an outgoing hole until tech and understanding increase allowing them to be visible and the ships getting protection. At some point it would get interesting because when navigation for one is discovered it would only be a one way trip until navigation is researched for the other to get back home