Just make it simple. The PS1 system worked wonderfully. We'll just have to a adjust it a little bit because there will only be three continents at launch.
Obviously, more continents/planets are going to be added as the game progresses. Each empire gets one specific warpgate that only they can enter and exit. The other three warpgates are usable by all three empires.
***For the first few months of the game before any continents are added, each empire must have one warpgate on each continent. This is to allow them to fight even after their "home" continent is locked. After new continents are added this will not be a problem, and each empire gets one or two home continents depending on how many are available.
There would be some benefits to this.
-Sanctuaries are better than footholds. They're saying these footholds will be "out of bounds" to other empires, which I assume means you get some stupid 10 second countdown to "get back to the field of battle, soldier!" and your screen goes gray. That doesn't make sense at it doesn't belong. ES warpgates WORK because there isn't some artificial out of bounds barrier that kills you in ten seconds, it just means this warpgate does not belong to your empire. You can actually fit that into the lore somehow. Just pulling something out of my ass, I can say that TR and VS nanites are not compatible and the warpgate won't let them through.
-You can stage an assault privately without fear of the other empires seeing what kind of units or how many you are amassing.
-A universal place to spawn and afk. You don't need more than one place for that, and the sanctuary could be a hub for other extensions as the game goes on. Virtual reality, outfit bases, outfit warship construction pads, etc etc.
-You can capture and lock continents from other empires. We can still turn that continent purple without having the fear of being backhacked as soon as we head out to the next continent.
-Probably many more I could keep listing.
Cons
-...uhhh... loading screen?? Waaah
The argument that sanctuaries slow down gameplay is extremely, extremely weak. I have never, EVER heard anyone complain about it taking a minute or two to get your vehicle and go. There are many more benefits to having a sanctuary than there are cons. And, when you come to think of it, there really aren't any cons. That's just nitpicking.