It is possible to have fighters stop entirely by pressing and holding a key. As for keeping it interesting, the mission would be designed with the shuttle in mind. Combat by the shuttle would be minimal and dilemmas would be presented e.g. the main ship has to respond elsewhere, then an enemy turns up and the shuttle has to hide or evade in a nearby nebula or asteroid field.
When I think of shuttle missions, I think of when they appear in ST:Voyager and other Sci-fi. The shuttle could be deployed in a battle to drop marines at a base, getting passed capital ships, or could have a device to disrupt their sensors.
I also think there might be times where it is safer to send a shuttle… perhaps to gain a sample from a particular nebula with radioactive properties…. Baryon nebula investigation? It could be that intense radiation would cause warp core failures on TSN capital ships, but a shuttle uses different energy systems (i.e. based on impulse reactors) that wouldn’t be damaged. Note, shielding would stand up to radiation, officer could be protected with an innoculation of some sort, or it could simply not be harmful.
I think there is plenty of scope to keep it interesting. The trick is adapting the fighter to become a shuttle. To me, it shouod have no torpedoes and perhaps one simple beam for defense. In otherwords, very little combat capability. That way it would be about clever piloting and completing objectives rather than having more combat capability. When the enemy attacks, it is better to have the shuttle aboard and officers on the bridge instead of attacking.