I think removing whatever is a mistake, the more stuff/ships/systems/equipment the better.
Make them dead end systems, implement the refered choke points,
and whille your at it, bring back all systems previously removed,
Why? Simple, the name of the mod is "Discovery",
Some peapole just like to explore and these systems could be a nice thing for those.
Also, may be nice for some RP, in the way that these systems could provide "homes"
for factions dont dont align with the already existing ones, so it might be interesting to see what would happen.
Basicaly, the more options the merryer, unless there is a server performance increase due to this removals i trully think the more stuff the better.