I was thinking (and this is probably a less that stella idea) you could make hyper tunnels between close stars. From what i understand the hyperlimit is caused by the interfearence of the stars gravity, two or more stars could cause a reduced disterbance zone between them and a safe(ish) path between them that can only be accessed close to the star (jump near star, sucked down path, spat out at other star) this would give an easyish (programming method) to travel to binary ect. stars with hyperdrives, while alowing/ forcing the choice of direct travel over indirect but posibly faster method (the quickest path is not always a stright line).
Actually you may be able to do a similar methodology to deter people from making really far jumps, if there was some sort of "link" between closer stars that increased the speed multiplier in that pathway, so that traveling to a star 10x farther away took 30x longer or something like that.
Another thing you could do is introduce hyperspace drag. Have the ship start out at it's initial speed X multiplier, and then constantly slow down, maybe to zero, or maybe down to some minimum like 10x the speed of light or something that would be useless for combat fleets, but would let you send One-Way probes or something like that.
The problem with that is the fuel situation, when you arrived at your destination would you be going your original speed, or if you slowed down 20% in hyperspace would your real-space speed be 20% less as well? I guess that doesn't matter all that much though, if you are moving through the system that would be annoying, since you'd have to spend fuel and speed up again, however most of the time you are actually probably going to a system to stay there, so you'd want to slow down upon entry anyways.
And actually, slowing down incoming fleets has the benefit of partially dissuading a drive-by genocide... if you know (and you would, because it would be distance based, and you know where the target star is, so when you set up the jump it would tell you your ETA and in-system speed on arrival) that you are going to slow down 20% in hyperspace and you want to make a (say) 5000 km/s attack run, you either have to accelerate up to 6250 km/s in the previous system, or make the jump at 5000 km/s, arrive at 4000 km/s and accelerate up to 5000 km/s in system. That costs 250 km/s less in delta-V, but the in system acceleration makes it more likely that the enemy will see you. Lastly you can just accept the slower 4000 km/s attack run, which gives the enemy more time to prepare after you show up on sensors, and makes all of your mass-based weaponry less dangerous.
