I remember a really good discussion way last year I was having with Frenotx and Golgot about variable supercruise mechanics, which was drowned out by the riot over Open-Only. Ima reconstruct what I remember, so hopefully at least some of it is the stuff I thought of too.
Very first, a return to deeper system gravity. This provides a system with more "terrain", to make system navigation something beyond "point ship dat way". Right now it's closer to Desert Bus in terms of gravogeographic effects; lots of nuthin. There's not much point in introducing anything that can speed travel or provide alternate routing when there's hardly anything to slow us down or move around as it is.
Variable and alterable supercruise profiles. Having one operation profile for all ships everywhere is boring and predictable; it provides little tactical, strategic, or shipbuilding consideration for flying across any given system arrangement. Variability is already reflected a small bit in SC turn rates, but could be extended to speed profiles as well, including accel and decel parameters. Throw outfitting (and yes haters even Engineering) on top of this, and now everyone has much more of a say in how their ship handles in the mode we fly it in most. It's almost a waste, how much work goes into our normalspace flight profiles by comparison.
Frenotx introduced an active-booster concept that would burn fuel and generate heat, with a risk of ship damage if you really push the limits. This allows a dangerous override to the above SC speed variability, so if you really neeed to, you can hurt yourself to get that extra speed. It also gives a neat use for fuel tanks, because really, fuel is laying about everywares in the galaxy and fuel scoops are pretty ubiquitous kit. Having a burn tank so you can boost your way into or out of trouble (even if you cook a little >__> ) seems like a fun thing and would give a more interesting reason to cart extra fuel outside of deep-space exploration or being really really paranoid about gassing out.
Golgot had an idea for insys micro-jumps which parallels the slingshot tunnel mentioned earlier; skill-based piloting at great hazard. It'd be even faster than a booster with no chance of interdictions, but the risk of being dead if you screw it up is waaaaaay higher. I'm perfectly fine with a faster but super-high-risk method being available, because Golgot's Space Coaster of Death would be fun.
While I'm wishing for things, I'd remove system wide scanners and introduce EWAR kit and counter kit to really add spice to SC, but that's technically outside the scope of this thread. It pairs extremely well with a varied approach to supercruise operation parameters however.