You could give the system limitations, like I did for the QSD in our camapign: you have to navigate to a specific spot, no variations -- make the calculations difficult or the pirce of failure high, so they don't want to use it as much. If it's a new system, make some of the difficulties higher due to unfamiliarity with how the system works.
Limiting them to what they can scan on sensors, or to areas with accurate maps of space would be good, too.
You can always dazzle the players with b.s. for why they can't just warp space and arrive in Andormeda in zero-time. And if they insist on power-gaming you...off their characters!
"War is an ugly thing but not the ugliest of things; the decayed and degraded state of moral and patriotic feelings which thinks that nothing is worth war is much worse. A man who has nothing for which he is willing to fight, nothing which is more important than his own personal safety, is a miserable creature and has no chance of being free unless made and kept so by the exertions of better men than himself."
John Stuart Mill