Hyperspace has been a bit rough the entire time it's been in Starsector. I think it's going to take a major revisement to smooth it out. Thankfully with this suggestion most of the work is simply shuffling around existing parts.
First, let's clear all this old hyperspace terrain off the map; now we just have our lovely swirly background. We're going to call those swirly depths "Deep Hyperspace". Oh yeah, and we have a bunch of jump points too.
Pick up all that flat cloud-ish terrain we swept off the map a moment ago, because we're going to put it under those jump points and all around them. Scatter some clusters of the stuff everywhere else while you're at it. We're gonna call it "Shallow Space". Real original, I know. Anyways, what this terrain does is reduce a fleet's sensor profile by half. It'll also protect fleets from some nasty deep hyperspace stuff described later.
We're also going to have two variants of this terrain. Shallow Space (Stable) and Shallow Space (Storm).
Storm terrain temporarily replaces normal shallow space. In addition to reducing sensor profiles, it reduces a fleet's sensor radius by half, reduces the speed of large fleets by up to half, and drains CR at a reasonable rate.
Stable terrain is formed around star systems by gravity. Unlike the rest of shallow space, it can't become stormy. Otherwise it's the same.
Alright, now we're going to bring back something that never made it in: wavefronts. Wavefronts occasionally fly across hyperspace, sweeping up small fleets in their path. Mid-sized fleets can power their way through pretty quickly and large fleets can basically ignore them. In addition to pushing fleets around, wavefronts also mildly drain CR. What makes all this bearable is that they only affect fleets in deep hyperspace.
Another hazard of deep hyperspace is the "Vortex". It's very similar to a black hole, except much less brutal on the CR drain and much better at sucking in small fleets. The special part about a vortex is the center - it's a wormhole to another spot in hyperspace. The vortex dissipates a few moments after it catches a fleet or after about a minute.
While it would be "cute" for wormholes to be a nonstandard game over by teleporting the player VERY far away, I recommend against any such feature in the strongest possible terms. Though let the in-game rumors fly!
You may have noticed we have yet to see any mention of fuel. That's because burning fuel to travel gets the boot under this revision. Fuel is only used to jump into hyperspace and for certain abilities. To keep it important, though, jumping takes a lot more fuel - like 10 times as much (as a baseline).
There is still a need for a limit on exploration time, to be provided by food. Food has been waffled about before, but this time we will nail it down. 15 crew consumes 1 unit of food per month. There, done. Oh, and finding more in the fringes of the Sector is rare. That pesky little 5 year expiration date at work.
Seriously though, food is a much better limiter than fuel, because you still have plenty of time to save yourself if you carelessly run out of it. Run out of fuel and, at best, you'll be doing a lot of waiting in the near future.