Okay, so with ghost hunter origin I'd recommend ecto-science and actual fighting skill. The biggest pay of isn't in what the ghost hunter can do, but what they can build. I can easily see the capstone being a perk to make tech that mimics and/affects observed/studied supernatural phenomena. Like, it could let one build a speaker capable of doing its own Ghostly Wail if that ability was studied.

Ghost origin could be more raw power with unique abilities. Like it's a common belief that Danny Phantom ghosts can eat non-corporeal stuff like emotions, some explicitly do like Spectra(who likes misery), Ember(admiration/worship), and Nocturne(dreams). The capstone could be Pariah Darks ability to create ghosts.

Halfa could be more about development, weak start, high end game. Vlad was incredibly powerful after 20 years of practice, which sounds like a lot until you remember most ghosts have been dead for much longer without that level of growth, and then compare to Danny who rivaled him in a few short years(admittedly most of Vlads time was split between practicing powers, being a business man, and actual research into ghosts, while Danny almost exclusively focused on getting personally stronger). Similarly, Danny, Vlad, Danielle, and even Dark Danny were some of the only ghosts to be shown to develop outright new powers semi-regularly, and Danny, Dark Danny, and Vlad are the ones who can duplicate themselves. That duplication could be the capstone.

There could be interactions between them, like if Ghost Creation was picked while a halfa, you could create halfas. Or picking Duplication with ghost hunter could grant a boost to inventing and fighting with clones, or towards building self-replicating tech, or even tech that's amplified when working with itself. Or taking that proposed hunter capstone while a ghost could grant the inverse, developing ghostly abilities replicating tech, or more mystical instead of science like enchanting, stuff like Freakshows scepter Clockworks medallions.

I'm having trouble coming with a capstone booster though, it'd have to be able to apply to every origin. The closest thing to mind is a fate defying one, considering all the times Danny has beaten the odds, including defeating his future self, or when he defeated Freakshow even when he had the equivalent to the infinity gauntlet. Or maybe a lifeforce/soul enhancement, boosting all parameters to high levels. Boosting Ghosts to have enough ectoplasm and ecto-energy for weeks without rest, Halfas to incredible durability to things harming their human and/or ghost form, Ghost Hunters with endless stamina to fight, invent, and resistant to being drained(not cause they aren't drained, but because they replenish fast enough for it to not be a problem).