I thought that the totem Pokemon came AFTER the Trial Captain? I'm guessing pretty much along the lines of what you said, they'll be gym puzzles essentially but bigger. Just imagine they condensed two gyms into one for each Island Trial, and after you beat the Trial Captain you get an opportunity to catch the local Totem Pokemon. Also beating an Island Trial is probably needed to unlock the Island Deity Pokemon on that island, like beating the captain or the Totem Pokemon makes it take notice of you and then starts roaming or hides somewhere on the island for you.
We won't know for sure until the games are out though.
