Currently, if you want to "raid" a supply or merchant fleet, you have to deal with all of the combat ships before you have a chance to get at the freighters. It would be cool if you could try to avoid the enemy combat ships by going around them and "retreating" on their "side" of the map. This would turn in to a "retreat" event with whatever made it across with chasing whatever the enemy didn't deploy, with whatever they did deploy in hot pursuit. Perhaps the ships that made it across would take a reasonably severe max deployment time penalty(EDIT: I mean peak performance time). It would also be cool if the AI could do this to you.
This could also be used to expand trading/player merchant gameplay. Instead of having trade disruptions directly affect markets, have them affect "trade routes" between markets. Spawn some pirate or faction sponsored raiders, have those raiders preform "raids" on merchant/supply fleets going on those trade routes. For the player, this means shipping goods between these two places temporarily is profitable, if they take the direct route with the risks that come from the raiders. If they go around, significantly higher fuel used can make it unprofitable, or hyperspace storms and maybe perhaps other deep hyperspace foes can make it equally dangerous. These things should be about as common and reliable as bounties if possible, and should only occur on hyperspace routes.
Perhaps bounties could also be worked into this, with big names with bounties on their heads raiding the trade routes, or with factions giving bounty for enemy ships killed on said trade routes. This could even go the other way, with a faction you are aligned with putting a bounty on all enemy merchant and supply vessels going on a trade route. This could also lead to interesting things with diplomacy and accusations of privateering.
Basically, make it reasonable to play as a merchant and raid other factions fleets.