How about leaving everything as is, but just either make the gravity wells larger or the units all slower and be able to jump to adjacent territories from anywhere on the periphery of the well.
This would work such that you still had to stop in well b on the way from a to c, but the stop was just to cool down and wait for the antimatter to replenish, ie in a situation trying to go a->b->c because a->c doesn’t exist, you charge the jump in a, jump to b, wait for antimatter return in b, charge in b, jump to c. Units or fleets transiting through b could be attacked while they were traversing but wouldn’t have to traverse all the way across the gravity well to get to the other "side." In this scenario and generally, how about increasing the time required to charge a jump?
