How about instead of removing places people don't visit ... You make them interesting to visit.
Everybody needs to go back through a trip down the memory lane and remember the days when you played vanilla. Why did you want to go out and explore? To read more lore, to see breathtaking sights, to find awesome wrecks full of strange and wonderful goodies? To say you have landed on every station, jumped every hole, found every trade route and every ship sell point? To enter the hall of fame as the man who has been at the end of the universe?
Remote Vanilla systems had a certain charm to them. And the fact that the campaign was made so you only got a tiny bit of a teaser of what else is out there, but never the whole package certainly helped.
The remote systems off the beaten path are the perfect opportunity where some PvE content can safely be introduced without anyone whining about stupid bots being in the way of their awesome RP.
So how I would approach this "problem" would be:
- make a list of all systems
- if any player statistic/heatmaps are available, exclude all well frequented systems from that list
- go through the jumps network - is the system crucial for getting somewhere important - if yes drop it from the list
- for the rest of the systems check forums - do official or unofficial groups have ongoing RP and development of those systems. If they do also remove those from your list
The systems left on your list are the ones people don't consider worthy of their time.
Some ideas of what can be done about those systems:
- turn them into PvE zones similar to the Omicrons where people go to farm Nomads (we might need a new kind of shinies for that!)
- if any environmental dangers are present (radiation, gas, dense asteroids) ramp them up to eleven and make some really expensive ore mineable there. Bonus points if you only allow freighters to go into the system through the jumpholes so people need to organize profitable expeditions using a jump module and a carrier (perfect opportunity for the Barge I've been hearing a lot about lately to make a comeback )
- turn them into battlegrounds where AI make constant war against each other, think Omega-5 in vanilla but much more dangerous to pass through. It would be an opportunity for salvagers to go collect guns and stuff dropped by the AI
- turn them into places where explorers go, full of fancy sights - maybe anomalies too so they have something to do there?
And finally maybe the starter Discovery map should have a bit less of the known locations. It's much more interesting to discover stuff on your own than have it handed to you through meta channels.