I would like to know why Vespucci is two jumps away from Stutgart? That's a fairly big route change for people going from Rheinland to Bretonia. Doesn't really promote interactions and makes the omegas an unused route between the two houses.
I don't understand Sigma-21 as well. This is now a solid link, though not legal, route between liberty and the sigmas. The point of the sigmas was to connect kusari and rheinland and not have liberty be able to have any interest in the sigmas.
A second change which might tie into the original 4.88 release is the Sigma-17 to Minor holes. That's a massive shift to suddenly have the sigmas directly connected to the omicrons core instead of just the omicrons concerning Outcast/Sairs.