Danny is similar to Kratos in the way of having busted Reactive Evolution that allows him to evolve against things he already has a resistance too but we don't assume he can evolve against hax he's not come across so the only things Danny has layered resistance to is Mind Manipulation (Above 5 layers), Biological Manipulation (Molecular level/3 layers), Soul Manipulation (3 layers) and for hax like Possesion (which works on the mind, body (molecular level), and soul) is 5 layers. Everything else is 4-D as well are baseline but can evolve going by his other abilities evolving.
But that's pretty much it. I can safely say Danny is the poor man's Kratos as the later pretty much has most of Danny's abilities cranked up to 11, far more skill/experience, better range, and a plethora of hax Danny hasn't encountered and thus doesn't resist. The only thing Danny has is the AP advantage but that can be closed with the exception of the Ghostly Wail which is 100x his base power but he won't start with it. So I can safely say Kratos either stomps or handedly schools Danny Phantom in the way of the Spartans.
Danny might gain new hax and resistances but we won't know until the 18 when I get my copy of the novel and see.