Yeah of course more hitpoints make a fight longer and not better... but hey, it is the standard method in most boss fights in video games Most of the boss battles in video games are only long, but not difficult.
Actually i used the "Moar Hitpoints" solution myself for all the aces in the FSPort Single Missions.
But to make a better opponent in general, you have to create an invidiual #Ace ship class of the specific Ace ship with other/better stats as it seems.
Special Hitpoints next to an higher AI class seems to be the best method to do without modding in the tbl files.
That's pretty much it, it's quite difficult to create a satisfying ace-on-ace scenario, especially under Freespace's combat model. Most fighters die in 1-2 seconds of sustained fire, so having a prolonged battle means that neither fighter manages to score hits on the other, which can quickly grow rather frustrating - see the SF Dragon.
So, unless you want to script the hell out of the fight, your options are rather limited :
1 - Give the ace a fighter & AI that's better than what you've faced so far, eg. a Seth while you've only faced Anubis so far
2 - Give the ace a fighter that's blatantly better than yours, eg. facing a Perseus while you're flying an Anubis
3 - Cheat and give the ace better stats compared to the base fighter, eg. special hitpoints & AI, custom #Ace variant, etc.
4 - Cheat even further and give the ace abilities you don't even have access to, eg. gliding, cloaking device, weapons it shouldn't be able to use, etc.
5 - Make everybody else dumber, eg. everybody's a lieutenant & he's a general, or everybody's using retail AI & he's using fury AI
And each of these has pros & cons :
#1 works alright in early-game, but kinda loses value upon replays.
#2 & #4 are effective, but rather obviously unfair.
#3 is rather tricky since you typically don't want the player to notice that the AI is cheating, which means you can't make the AI too strong compared to other fighters of the same type, otherwise you might as well say the AI has a super custom fighter & you are back to #2.
#5 means you are potentially sacrificing the quality of every other fights to make this one more satisfying if you are not careful. It should work if you are going for a more arcade-y feel though : drop everybody like flies, then this guy shows up.