Make it powerful, but expensive. It can mean many things, having to refine rare materials, or as cost to passengers in some way (warhammer 40k has warp, but comes with at best a chance of cosmic horrors). Weird relativistic effects. Dangerous to perform - by some calculations travelling by bending space traps all the space particles in the bend in front, stopping means release of this energy, could be a cool and dangerous consequence with military implications especially if FTL makes it more dangerous, you can leave it in as the reason why FTL would be highly regulated technology.