See, the problem with a lot of these suggestions is (deliberately or not) that they're all cribbed from eve online. Even if it was accidental, perpetuum does walk a similar path and there will always be some cross over. That's not inherently bad but perpetuum needs a unique selling point in the endgame - something for potential players to hear about and go 'oh god yeah, I want some of that'.

Focussing on mechanics that perpetuum doesnt share with The Other Game seems to be the way forwards - the cover/Los mechanic is pretty nifty, and also means there is the potential to fight ~inside huge player built cities, factories, research or communication outposts. But building a base and going inside arent all that exciting, everybody has a base of some sort. Perhaps you could physically steal research or resources in daring raids on these structures. Negotiating with whoever 'owns' the island to pay them rent for building a communications outpost that provided intel on bots passing through, or just throwing structures up and defending them when the neighbors came nocking.

I dunno, perhaps enterable structures arent the way to go, perhaps the perpetuum endgame should be based out of giant nomadic sand crawler type machines (without doomsday weapons obv;)) that can redeploy your entire corp much more quickly. Maybe structures completely suck and the real endgame is all about building very expensive robots to pvp in, or in enslaving other corps, or simply posting lots and insisting that makes you famous.

I don't think any one killer feature is needed, just more sand in the sandbox.

Random aside: You mentioned intrusions - Incursions in eve were an interesting feature actually - I ran a lot of them in hisec and lowsec because they were a total isk faucet - and the overwhelming feeling was that lowsec was simply an opportunity for the larger corps to get richer, and high-sec public fleets were filled with guys who mutually loathed each other, marshalled by equally loathed self-appointed FCs whose FCing ability ended at remembering the order you needed to shoot things and stay at the keyboard 23/7. They were broken because whilst a pretty cool idea and a great way to earn isk, they didn't encourage the non pvpers to pvp after the first fleet was welped, and they didn't lead to lowsec population rising.

And yes arga, 3k posts do stand for something albeit not quite what you think.