I'd like to first thank my dear friend 
Ahem.
The following rant contains spoilers for Persona 4 and 5, Shin Megami Tensei IV Apocalypse, Final Fantasy IV, Earthbound, Mother 3, Mega Man Star Force 3, Ocarina of Time, and Majora's Mask. If you don't want spoilers for said games because you haven't played them, please stop reading now and now you have my unmitigated pity for being denied so viciously. If you don't care, proceed.
It's the final boss battle of a JRPG! The Big Bad Evil Guy is letting loose with every top-tier spell and attack there is, and probably a few unique skills styled after theoretical end-of-the-world scenarios, religious apocalypses, obscure astrophysical phenomenon, or just really unpleasant things- i.e; Big Bang, Ragnarok, Creation's End, Supernova, Irretrievable Eyelash in Eye, etc.
Needless to say the party is having to bust out all the limit breaks, really expensive spells, and the full heal items they've hoarded like a dragon... or use the really cheesy strategy that allows the physical powerhouse to attack eight times in a row for absurd damage.
Suddenly the BBEG says something to the effect of 'okay, that's enough of a warm up' and hits everyone for damage that exceeds any reasonably expected HP total, bypassing the defenses of the ultimate armor you've spent hours grinding for the rare materials to take to the blacksmith who lives on that really tiny island on the edge of the world map with only a chain-smoking mascot animal to keep them company. Those abilities you have that allow you to survive a lethal hit once? Not relevant here.
You all know where this is going, but I'm obligated to type it out anyway. Everyone the protagonist has a bond/friendship/follows on twitter calls out to them! "You can do it!" "Don't give up!" "You can't die! You still owe me twenty bucks!"
The battle might conclude with the hero blasting the ever-loving Worcestershire sauce out of the BBEG with the power of friendship, or if the developer really wants to hammer home the moral of having friends, the BBEG will spam every attack they have (or maybe just the prior one-hit kill) to no effect, with an obligatory exclamation that they never saw this coming! "How can this be? I'm omnipotent! I paid like a hundred bucks for the Protagonist Killing DLC package!"
Cue Kirk summary by the hero's friends, the wrongs being righted, the end credits, and a New Game+ so you can go back and one-shot that one gimmicky boss that boiled down to praying to the Random Number God.
You've all seen this before.
Ultimately what this kind of narrative device does is reduce other party members to an optional thing, meaning that if a player is patient enough to grind until the absolutely necessary party members, often only the protagonist, are capable of weathering the final boss' attacks, then the power of friendship and allies kind of falls flat. It all but flatly shows that only one person is capable of unlocking the power to deal the final blow, which while it can set a protagonist apart as the 'chosen one', it can also feel like the entire plot of the game comes down to 'our win button vs. the bad guy's win button'.
Sometimes, admittedly... this is what people actually want. Friends and allies rallying to tell the Enemy of Life, Liberty, and puppies and kittens to suck it. It can be a powerful and emotional conclusion to a long tale of hardship- when done correctly.
In other games, however, the power of friendship is strong, but isn't the definitive win condition. The BBEG might decide to open up with Youdienowdynega right before the battle starts, and only the prayers of your allies can revive the party to fighting strength- alternatively, your allies could be otherwise occupied distracting or debilitating the final boss, giving the opening needed to deal damage it can't shrug off.
Dealing The Final Blow Examples
Persona 4 and 5's original stories have final bosses that will, as per Atlus tradition, require careful strategy and high levels to bring down. However, at a certain point, these bosses will say 'that's enough of that' and proceed to wipe the floor with the party. Persona 4's variant on this requires either the emotional resolve of a cold lump of stone or a box of tissues to get through, so be forewarned. Then cue the emotional speeches from the protagonist's friends urging him to get up, and of course, calling down divine or diabolical fury on the offender.
This is by no means a failsafe should the party fail to last long enough and do enough damage to get to the aforementioned threshold. A party wipe beforehand is treated like any other game over before hand. The player must earn the right to push the "I win" button.
However, only the protagonist can deliver the killing blow, meaning everyone else there is simply to accelerate the process of getting to the point where the hero is desperate or enlightened enough to push the win button. Having the boss shrug off the numerous attacks thrown their way as well only seems to reinforce the idea the final boss was allowing the battle to progress because they were bored.
A notable variation on this execution can be seen in Mega Man Starforce 3, where the player must beat the final boss of the main campaign in a fair fight. It's only after the boss revives, a touching cutscene, and the protagonist going into permanent 'super-mode' that we have a battle in which it's literally impossible to lose, and it comes across as an awesome conclusion to a series rather than shoehorning in a speech about friends.
"It's up to you now" Examples
Final Fantasy 2/4 has the people the party has saved, fought with, and otherwise had relatively amicable encounters with pray for their survival right after Zeromus shrugs off a double-dose of Meteor to the face and retaliates with "(Insertcoolnamehere)ja" to prove he is, in fact, end boss tier. Friends, departed loved ones, and lost brothers all send their prayers to revive the party from death and help reveal the boss' true form, but from then on out, Zeromus must be brought down through sheer brute force.
In more single player oriented games like Ocarina of Time and Majora's Mask, sages, giants, and princesses will aid Link as best they can, but it's up to the player to remember every trick, counter, and tool they have to overwhelm the boss.
In these cases, the 'power of friendship' gets it's due, but no amount of warm fuzzy feelings will make a dent in the bosses' HP. Whether preventative or restorative, the deus ex machina only occurs at a set time and only once.
"Only The Button Matters" Examples
Earthbound is quirky. This is not an insult, it's a statement of facts. Earthbound wears its quirkiness as a hard-earned badge of honor, and provides a completely different final boss experience to boot.
So the hero has accumulated the power from eight key points in the world, gone through a dream-like epiphany, and went through a power-up sequence to boot. Surely it's going to be a full-blown slugfest of a final boss battle, right?
Not exactly.
Two of Giygas' phases require the time-honored strategy of 'hit it until it dies'. Afterwards, while attacks will inflict damage, his HP is effectively infinite. Giygas can only be beaten by repeatedly using 'Pray', which prior to the final battle was the obligatory 'random effect' skill, just as likely to harm allies as it was to help.
The battle then becomes about keeping Paula, the only member capable of praying, alive long enough to call on everyone to help. There's a brief hint given right before this point as to what to do, but after a certain number of prayers, a message appears giving indications there's no one left to pray to, potentially tricking the player into thinking they haven't got a prayer.
Mother 3 defies this and plays it straight in the same game- the fight against Porky is a straight-forward beatdown requiring tactics on par with most 'serious' jrpgs, but after having his war-machine broken, the time-withered Porky withdraws into an Absolutely Safe Capsule, which takes only 1 damage from any attack, but has no offensive ability whatsoever.
The battle after that is something that I will not try to put on paper. It's less a battle and a reconciliation between two siblings that requires a pacifist approach, something that needs to be experienced rather than explained.
"Repeated but moderate" Example
Shin Megami Tensei IV: Apocalypse has your party members aid you in both a mechanical and narrative aspect- throughout the game, you can set an ally to provide support between turns, be it additional attacks, buffs/debuffs, or healing and support. But in one route where you take the fight to YHVH, you must have your allies denounce the Evil Giant Golden Head Of Doom to do damage.
There's also another party tackling the final boss alongside your own, for an additional feeling of a grand finale against an oppressive Demiurge. If this sounds too lenient for an Atlus game, play the game on Apocalypse difficulty- preferably after per-arranging an appointment with an anger management therapist to help you recover.
In this scenario, everyone is shown to be necessary, even the ghost of the pervert who died while being a peeping Tom. Every actor is shown to have a part to play in taking down the final boss, all while the fight requires a full understanding of how to make the most of every turn, having a proper setup of party members, and being sufficiently powerful enough to both dish out damage and take it.
Convoluted Conclusions
I admit a bias towards having party members who are there to fill roles the protagonist cannot, or better yet to have a game designed in such a way that the player decides who will be in the final party, with the answer of if the day can be saved answerable by a matter of sheer preparation and tactical understanding rather than any vestiges of Deus Ex Machina.
This, of course, is all merely opinion. A major part of the RPG is the storytelling element, and "they hit the demon king until he died" isn't the most dramatic way to finish the battle.
There is always a delicate balance that must be considered, deciding what should challenge and what should entertain the player. Ultimately, what it boils down to is a question of "did you have fun"?
And if you can answer "yes" to that, everything else is a matter of taste.