I haven't made too many of these missions in the past, so I'm only running on limited experience here, but I'd offer a couple of thoughts.
First, pick a good ship. What you ideally want is a big, complex ship with lots of things for the player to do on the way to blowing it up. Lots of turrets, subsystems and destroyable submodels. I'm also a fan of geometry that provides a degree of mission scenery, in the form of large scale detail that gives good geometric contrast. It's a hard concept to explin, but basically if the geometry provides lots of places for the player to manoeuvre, and relatively few areas of long flat expanse, it's probably got it. This makes the actual flight mechanics more interesting, and is one of the good things about, for example, Slaying Ravana
Second, and again before you even start the mission, do what Matth said and set it up. Have the player encounter the ship at least once before, get him to become familiar with the ship. This can be achieved by telling in Command briefs or cutscenes, but is better done through in-mission events. [V] did this well for both the first Sath and the Ravanna. Having the player recon the ship can also be a good idea, like the Lucifer, if it's got particular attributes of interest (generally either very high detail or a very large scale works). Avoid the recon for well known or small ships, IMO.
Thirdly, when you come to make the mission, ensure that the player has a task at all times. This often means targetting specific subsystems (engines, turrets and hostile fighters mostly, but whatever else you can make work with the model and the story is OK too) rather than just being given a huge number of hitpoints to chip away at.
Fourth and finally, balance is, as always, probably the most critical thing.
So, those would be my suggestions. Some of Matth's plot related points are important too (the opposition choosing to escape and being tactical), but from a pure FREDding perspective they're less important (much more important to the narrative though). IMO, get these four right and you'll have a reasonable mission, most of the time.
Some additional points you might want to consider:
You don't always need a capship on your side. Maybe keep the friendlies out of the battle for awhile while the player is disarming the big guns.
One way to break up the inevitable monotony of attacking the same ship repeatedly would be to give it some backup. Hostile capships arriving halfway through the battle give the player a new target, and if they're relatively easy to defang or otherwise eliminate, they shouldn't be too diverting from the main job.
Remember that you can rebalance your hostile super-ship for this mission, and you'll probably want to. The first time you see it, consider special-hits, mission-specific weapon variants, adjusting the armament or a unique armour type (if you're using it) to make the battle harder or easier than other battles that might feature this class.