Curious how things will play out. I was uncertain at first whether we will battle the Captains or not since it sounded like Totem Pokemon were the last thing to do, but reading it over again, it could be that the Captains challenge you after you defeat the Totem Pokemon. If anything, they could be optional battles.
But I could see a case of Totem Pokemon using only one ally each, and the Captains use two Pokemon each, while the Kahunas use three each. If we assume there is at least 8 Captains; and as such 8 Totem Pokemon, then the amount of Pokemon used would be 44, which is the same amount of Pokemon used by Gym Leaders, Elite Four, and the Champion in XY.
Totems
I would assume Totem Pokemon's allies will basically just be their pre evolutions, and I imagine they would all be Gen 7 Pokemon. With that in mind, so far we know:
Normal-Gumshoos(Totem), Yungoos(Ally)
Grass-Lurantis(Totem), Fomantis(Ally)
Fire(Only know Type since it should match Captains)-Salandit evolution(Totem), Salandit(Ally)
Water(Only know Type since it should match Captains)-Yet to be revealed Pokemon
Electric(Only know Type since it should match Captains)-Yet to be revealed Pokemon
Captains
For Captains, we know Kiawe has a Marowak; since we know he is a Fire specialist and Marowak has an Alolan form which is Fire, it's safe to assume he has that kind and as such maybe each Captain has a Alolan form Pokemon and a Gen 7 Pokemon. Also, since Alolan Marowak is prefect for Kiawe design, I would hope that each Captain have Pokemon that fit them(Albeit, that hasn't happen much with other types of characters):
Normal Captain-I assume this will be on the first island and likely the first Captain so the Pokemon shouldn't be too strong. Better idea when we see the character, but right now no option for Alolan Pokemon, but maybe has a Stufful or Pikipek/Its first evolution.
Mallow-Most likely the first Captain on the next island we go to, and probably still we be fairly early in the game so still shouldn't be too strong. Bounsweet/Its evolution or Morelull/Its evolution and a new Alolan Grass type(Don't see Exeggutor happening). Being a cook, Bounsweet and Morelull would fit that well.
Kiawe-Hard to place where he'd be, if Alolan Pokemon evolve around the same time as their original form then it should be around level 30 which Guzma is at when we battle him at the start of the third island so he may be the last on the island. Alolan Marowak should be used, and I'd say a yet to be revealed Pokemon.
Lana-Seems likely she's near the waterfalls so she sould be after Mallow but possibly before Kiawe, depending how far apart the levels will be. No Water Alolan Pokemon yet, but Wishiwashi for her Gen 7 Pokemon, she looks like she'd use Fishes.
Sophocles-I imagine him in the observatory on the big island. Maybe Vikavolt and Alolan Raichu, but I kind of have a hard time seeing him with them, more so Alolan Raichu(Mainly because Sophocles looks jerky and Alolan Raichu looks friendly, but he does have a Pikachu key chain(But also an Electrode).
Kahunas
Hala-Hard to say what he'll use. It seemed like he would use Electric because of Tapu Koko choosing him and it seems like the kind of thing GameFreak would do, but Sophocles uses Electric. So I suppose maybe mix. Whatever the case, I'd like to see an old Pokemon, an Alolan Pokemon, and a Gen 7 Pokemon. He'll be the first Kahunas battled, and it'll be early on, so he can't have too strong Pokemon. Not sure what to expect Pokemon wise for him. I could see Alolan Raichu with him, maybe Rockruff/its evolution, and really not sure for an old Pokemon.