The main things were:
1. The communication-speed (commRelayMessageSpeed) issues with Market updates (in particular, Missions / Bounties being severely out of sync, to the point that you'd get a Mission on the Intel screen, go there and discover it was long-gone).
2. Communication range (commRelayRangeAroundSystem) being arbitarily short meant that Colonies might not get Missions at all, because they weren't "connected" to the Core. In non-Nexerelin gameplay with just one added Faction, this is actually a real issue; the Core's the source of most Missions.
Basically, though, things break, when Markets are arbitrarily too far away from the Core, but we're still using 100% Vanilla systems under the hood. I don't think Vanilla should have a concept of "hyperspace message speeds" or "hyperspace message ranges" in it at all; this is needless complexity in what should be a straightforward mechanic, imo.
The other two settings were more for convenience than anything else; I was originally going to allow for Hyperspace-based Factions. I don't have that supported currently, so I'll remove them.