I propose a single flat universe, partitioned in concentric zones centered around the core.
Z0 zone (core): anything goes
Z1 zone: anything goes, except any power creep is temporarily "downgraded" into it's Level 1 equivalent (until it returns to the core zone, where it's reinstated)
Z2 zone: powercreeps have no abilities at all.
Z3 zone: T3 boosts have the effect of a T2 + the restrictions of Z0 to Z2 apply.
Z4 zone: boosts have no effect.
etcetera. essentially, like the "zones of thought" from Vernor Vinge series.
Every now and then the zones expand.
- new players on the outer rims don't need to deal with the full complexity. However if they survive in one place long enough, they'll be forced to.
- experienced players can't project their full power to any point on the map though portals or jump rooms, it's restricted (based on the skill level of the neighbourhood)
- there suddenly is real estate worth fighting for. Being in the center has economic advantages (as well as risks)
- outer players can fight the center on equal footing and gradually test new things (even if boosts have no effect, they can still be applied outside, and become active inside. same for power creeps)
- easy to explain, easy to reason about, increases game depth, and (I think) reasonably easy to implement.
This mechanic offers lots of room for further tweaks to balance gameplay.
For example, it would be fun if zones can change shape unpredictably or due to in-game events (lots of creeps lost in a block -> downgrade the zone. lots of GCL praising -> increase it. etc)
Zones could have different levels of minerals and power, etc.