Supercruise should be the fuel-efficient method of intra-system travel, with the added benefit of fuel scooping, exploration, unidentified signal sources, and interdictions (if they can be classed as a benefit). However, it does take time, so intra-system hops could bypass such tedium. However, there should be risks and costs involved.
What kind of costs?
Opportunity costs:
- exploring
- unidentified signal sources,
- interdiction(if that's a cost),
- fuel scooping
Resource costs:
- Fuel usage
- Increase FSD repair frequency
What kind of risks?
Short hops could greatly increase FSD wear and tear, thus increasing the likelihood of misjumps.
Those jumping intra-system probably have reason to avoid interdiction, so they would be prime piracy targets and/or potentially seen as suspicious by police.
How could this add to the game in any way?
Navigation beacons would finally have a real use as endpoints for intra-system jumps. Using them would make it simple for police/pirates to detect and scan travellers whilst still well outside no fire zones, however.
Perhaps certain outposts don't want nav beacons nearby, so you still have to SC to such places.
Beacons might be occasionally towed elsewhere for nefarious purposes, or even jammed/spoofed. This would be a good way to organise ambushes and stop traffic in a system.