Best upgrade to decrease in-system travel time?

Sometimes a straight line isn't the fastest way. Gravity wells can slow you down massively, especially gas giants. It is better to do a curve around than crawling through the slow zone close to them. When you are leaving a belt at a gas giant it is always better to leave its proximity and then go around towards the station.

Also note that "slow down" is a notification and not a command. It's already too late to slow down when you see it. Time for a loop. Gravity well effects and slow down are not very transparent, especially to a new player. It needs experience and practice to handle and use them well.
 
Traveling above/below the stellar plane (term?) in an arc to avoid gravity wells helps drastically when crossing systems. Far easier with head tracking, but not hard to get used to without.
 
If you settle in one system for any period of time, say to rank up with a faction for one of the Engineers or to get higher paying missions from being allied to the factions based there, take the time to look on the mission board. Take note of which systems commonly come up as mission locations and jump over to them (you only need to jump to the main star and go no further) and scan the system.

Now you’ll have a good idea of which systems will require long SC flights. As Para Handy says, most missions will give you the location distance but Assassination missions and some scan missions will not - but you’ll now know which systems to avoid taking those missions in.

N.B. Assassination missions will have you searching USS so you‘re not just looking for planets, a secondary star 200’000ls away will potentially mean a painful SC cruise just to take down one Expert Viper.

That advice may be slightly off topic and perhaps be for missions you’re not yet taking but if you dislike long SC journeys it’s worth knowing now.
 
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