Personally I'm a fan of "fold drives", that is you basically make your own worm hole and fold space around yourself. A great gameplay limiting factor can be the distance you can safely fold in one go.

Put in a mechanic to allow the players to 'risk it' and push their drive beyond what is considered 'safe', such as a DC5 to extend range by 10%, DC10 for 15%, etc. The more you push it, the more extreme the risks and consequences of it become. All the way up to "Your party's atoms intersect with those of a Star's core, and you have just ripped space-time to cave in 20 stars. On the bright side it was recorded by astronomers, and the known universe will always remember you when they pass near the massive navigation hazard you have just made."

Less critical failures could be damage to the party/ships systems.

Gives you upgrade paths, however it does require you to 'map' your stars of interest and have things large enough that a better engine will actually matter. Another restriction may be to require to be within a solar system, and jumping to a spot between stars would leave you stranded. (Another good option for pressing your engines too far. "Opps, you got greedy and missed the star. With sub light engines you are now 954.32 years from the nearest star. How much food did you say you packed?")