In the case of something that could jump you across an entire system, thus granting you the ability to avoid pirates, PvP, mission-related interdictions and turn Cr50m/hr missions into Cr500m/hr missions, it'd need to be a doozey of a drawback to balance the benefits it'd provide.
Frontier's original pre-supercruise idea for in-system microjumps had the concept of pirates being able to lay a "net", presumably across the predictable travel routes between points of interest, and micro-hyperdict passing ships.
So rather than simply evading the interdiction, or getting a fast enough start that they're left behind trying to get out of a planet's gravity well ... it's a case of dropping out unexpectedly at a random point in space right in front of a pirate's guns, with the full drive cooldown before you can move on.
Add to that the original plan that being shot - by anything, even with shields up - would disrupt and slow drive charging, and you'd generally have had to actually kill the NPC pirates to proceed.
Also, you'd have appeared in system at the nav beacon - with whatever else was there - rather than safely in supercruise ... and had larger journeys to get to the station from the microjump drop point, rather than being able to drop out of supercruise almost inside the NFZ.
Vital as supercruise has been for proper exploration - and I can't imagine how planetary landings would have worked sensibly with microjumps - the 11th hour decision to use it rather than microjumps did interfere with a lot of working game designs, some of which still haven't really been resolved.