Delta Episode wasn't the first time Gamefreak dabbled in scripted fights. The first was clearly Black/White.Hmm... this actually doesn't sound too unrealistic. As far as I can remember, Rayquaza will be forced onto your team in the Delta Episode, giving you no choice but to swap out a team member.
Meanwhile, in a completely different game: The third and latest iteration of the Dark Souls series (fittingly called Dark Souls III) features a boss with a titanic amount of health and defense. Bringing him down is a lengthy test of endurance and skill, since being a Dark Souls boss, he can take you out in a few hits. That is, unless you pick up a special sword lying in his boss room. The unconventional sword nullifies the boss' defense and deals an enormous amount of damage, though it requires some... unconventional use.
This boss battle got some flak for being a scripted battle in an otherwise very flexible game series, but for many it worked well nonetheless. It is far from the only scripted battle in gaming history, but a good and recent example.
It could be that Game Freak wants to try out something similar. A climactic battle where the only way forward is the attack that cancels the opponent's Ability. You catch the cover legendary, it is forced onto your team, maybe even positioned in the first slot. The UB attacks, and none of your moves seem to affect it. But your trusty friend stands on the sideline shouting "Nothing seems to bite! Perhaps Solgaleo's Sunsteel Strike will harm it!" in bold and blue text. And then special cutscenes play and everything is epic, if not for the fact that the only way forward is to follow the script.
But, like the battle in Dark Souls III, other strategies can yield a win too. If you play patiently, conserve your items and use clever strategies, it is possible to hack the boss to death without ever picking up the special sword. The obvious path is pointed out clearly, but if you look for alternatives, they are there. Having Mold Breaker, or using Substitute cleverly, PP stalling until Struggle or other strategies might win too, creating an extra option for the savvy player even though the opponent might have titanic HP and Defense, no weaknesses, and an ability even Shedinja would envy.
Based on how Zekrom/Reshiram are almost forced into your party in the first slot it's pretty clear Gamefreak wanted a battle of legends at N's throne room. And the battle is very much in your favor for doing it this way, N's dragon is two levels higher which is to his disadvantage since if he chooses Fusion Flare/Bolt he'll go first due to higher speed stat. This allows your own Fusion Flare/Bolt to power up and easily kill his dragon in a few rounds.
But like the aforemention Dark Souls, you can totally ignore the legendaries and fight it out your way with your trusted team of 6. They even go the extra mile of giving an even harder boss in Ghetsis right after N that seems set up to punish you if you rely too much on your legendary dragon (Cofagrigus will likely hit it with mummy and Toxic, and if you still try to muscle it out then Hydreigon will kill it outright).
So if that's what Gamefreak thinks a scripted boss fight is, then I really wouldn't mind if they returned in Sun/Moon. And if they aren't over used and properly built up, scripted fights can be really great for interactive storytelling. Mother 3's final boss is completely on rails and still makes my eyes water just having to watch.