Part of it is the interface (it would be nice if we could toggle slow movement, and even better if we could set our fleet speed to s specific setting. I don't mind the intercept fleets, but as much as I love the game overall, I really hate hyperspace storms and how so much of space is filled with them.
"Go dark" instantly halts your fleet to slow speed, with the added benefit of reducing sensor profile, you can just toggle sustained burn/go dark as needed. Hyperspace doesn't normally spawn intercepting fleets outside of missions, just the ambush ones, they are a bit predictable in where they appear, most commonly at the end/between slipstreams.
As for storms themselves — I obviously can't know for certain how Alex envisioned hyperspace travel, but I'm somewhat confident in saying that for long distance travel its not intended to just click on a desired system and enable autopilot to take you straight through miles of death clouds. You are meant to read the hyperspace map layer and spot multiple open paths that you can take around the main storm bodies.
So here's my problem with making hyperspace travel more inconvenient (or challenging, if you prefer to think of it that way).
For the game to make you spend a lot of time in something, it has to be a fun minigame for at least some minority of players.
Here's an example. Some players hate piloting their own ship. They prefer to focus on building an AI friendly fleet, and fitting their ships with AI friendly loadouts, picking all the "big-picture" leadership skills and nothing in combat, etc.
Some players prefer to directly control their ship. They pick combat skills, and they think of their fleet as just a meat shield / distraction so they can be the hero and kill the enemy.
Both approaches are valid. Combat is fun for both playstyles and that's great!
Ok here's another example. Say someone likes to get to colonies asap and micromanage like a 4X game, maxxing their passive income and fighting off colony threats. Some players prefer to play as a smuggler / space trader / missions / etc. Again, both valid play styles, colony management and missions are both fun.
Now here's my point - is there anyone who plays Starsector because they want to spend MORE time in hyperspace? Does anyone go "this hyperspace minigame is really fun, I want to spend as much time as I can mapping slipstreams and plotting the optimal course to avoid / exploit storms"? Or does every player think of hyperspace as sort of an inconvenience to get to the combat / trading / missions / exploration that they really want to do?
I am completely open to the possibility that there are a lot of players that actually think that way, though I certainly cannot say that I'm one of them. And I think of myself as a player that really likes exploration. The difference, I think, is that exploration offers lots of positive awards. Navigating hyperspace is a game of "is this slightly inconvenient, or really really annoying"? Probably the closest thing to a joyful moment in hyperspace for me is coming across danger beacons. I'm happy to see a danger beacon, because that means I've found an interesting system, one that I know is worth surveying. And that's fine actually - if hyperspace is an obstacle we have to surmount to get to something we want to get to, that's fine, but I guess I can't say I would want to spend a lot more time there than I already do.