Well, Acerola was the island captain available to sub for Nanu. Sophocles was also a likewise new captain so he couldn't leave his post.
Nanu is in his Kahuna position because he couldn't refuse to turn down Tapu Bulu's offer, since the Tapus are who choose the Kahunas.
So - Today, I Learned that it's the Tapus' fault(s) for messing everything up! -.-
Thanks to both of you for clarifying! Alola's lore seems interesting but unwieldy.. Yeesh, the mere act of forming/having an Alolan Elite 4 seems like more trouble than it's worth, given all of these restrictions and the Tapus' perceived interference (Alolan people may not see them as interfering, but I sure do.. @_@) And Nanu must be miserable..
I would prefer Alola's Elite 4 to be 4 not-seen-before Pokémon Trainers (and the proto-Champion/Champion being someone that the player has interacted with before, as is tradition - although as a side-note, it would be a neat twist for a region to have a Champion that the player hasn't interacted with before, with an Elite 4 that the player has interacted with before but not in League-battle capacities). However, that Elite 4 implementation may or not clash with the concept of Alola's League being a nascent one.
In any case, I don't know why Kukui even bothered to make a separate "Elite 4"; just add 1 more Trial Captain (maybe Ryuki or Kahili or some new Ice-type user. Alternatively, just keep 7 Trial Captains and plop Ryuki/Kahili as a Battle Tree facility head) and you have a group of Trainers that can serve double-duty as League heads - 8 Trial Captains as 8 Gym Leaders, and 4 Island Kahunas as the Elite 4. You also have a unique interesting League arrangement for variety (For each of the 4 islands: 2 Gym Leaders, then 1 Elite-4 member. You might have to fudge around with levels and level scaling though - fighting someone like Sidney when you've just beaten Roxanne and Brawly would be a bit too rough..). Consequently, you match the typical number of non-Champion League heads: 12. Aside from the aforementioned leveling/scaling issue(s), though, the only other downside that I can see is that Mount Lanakila's summit would be a bit emptier if it only housed the proto-Champion/Champion...
As an aside, I find it interesting that the total number of Alola's unique Trial Captains, Island Kahunas, Elite 4 (only counting Kahili since the other 3 Elite-4 members already have active island-challenge roles) and Professor Kukui the proto-Champion, 13 altogether, matches the 13 League members typically seen in other regions (8 Gym Leaders, 4 Elite-4 members, and 1 Champion.
Also, it kind of bothers me that the amount of Trial Captains isn't evenly spread across the 4 islands of Alola.. Like Game Freak, couldn't you have made just 1 more Trial Captain to have a "2 Trial Captains and 1 Island Kahuna per island" layout..? :/. This is like the one region where we actually need the number of Trial Captains/"Gym Leaders" to be 8.. XD. The other regions could've sufficed with 7 Gym Leaders (although I'd hate to just remove a Gym Leader like that since I pretty much like all of them - then again, Kalos Gym Leader Valerie's design reminds me way too much of Hoenn Frontier Brain (Battle Pike Queen) Lucy's design, which was first, so... :x)
Not to mention teams with actual movesets instead of just the copy/paste level-up moves. Seriously, after Victory Road in ORAS and Vast Poni Canyon, I'm hoping this doesn't keep becoming a thing.
By this statement, do you mean that the implementation is that the foe Pokémon only have the 4 most recently-learned moves from their level-up move learnset in their movesets (that one would expect them to learn at their current level. For example, maybe a Level 40 Fire-type Pokémon knowing Fire Blast, Flamethrower, Flame Charge, and Ember) rather than a competitively-geared moveset (like just 1 Fire-type offensive move and the other 3 moves being something like offensive moves covering types that Fire can't or status moves to raise the user's own stats or debilitate the foe via lowered stats or a hindering status condition?). My apologies if my inquiry doesn't make sense.. :x