People like big events.
Big events in space are BIG so there is bleep all you can do about them. No way to interact with them so who cares?

Let's say there is a chessboard galaxy and on A1 there is a super neutrino novatastic kaboom or SNNK because that rolls off the tongue better.
A shockwave now expands through the universe, destroying everything on A2 + B1, then B2, then...
I think that should be big enough to satisfy everyone wanting Big Events.

If you build a protective generator - specially built for this particular SNNK's wave spectrum - in a star system quickly enough, this system becomes immune.

If you build a counter-SNNK generator and toss it into the the system's sun, you generate a counter pulse which doesn't destroy any star systems of it's own but eats up the SNNK's wave front where it hits it.
This way you can shield an entire cone of star systems past that point.
More effective... but the inhabitants of said star system may not look too kindly at your plan of making their sun go boom. Lowers real estate value and all that.


Also, this generates a lot of new and undeveloped frontier once in a while.

I remember wishing there was a quest/mission for X3 that would bring on sort of an lategame struggle for well established players. Have some broken down gate somewhere, kind of like the Hub, and after you put in a ton of time repairing it, you open the gate, go through, and.... Xenon. Everywhere. Congratulations, you just opened a gate into the Xenon home sectors, and they are NOT happy about it. And from there, you get a titanic struggle to protect the galaxy from this incursion. Something that can only be defended against and pushed back by players who've been amassing fleets, have massive infrastructure, etc.

I know there were a couple of mods like that, but they were just new game modes that you had to deal with from minute 1, rather than something you initiated when you felt up to the challenge.