New-ish DM. DM'ing for a group of 6, different levels of familiarity and skill set for a game. 
Classic fantasy adventure.
Every character is currently lvl 4.

Currently planning an ecnounter, where they have to clean out a merrow and sea hag nest from the ancient half-sunked fortress and find a "controll room" for a giant stone knight figure oustide. 
Some time, before entering a dungeon, they will briefly encounter a zombified dragon turtle, and will be alerted, that it's currently coming towards the dungeon. Entire adventure will culminate in one of the players taking control of the giant, as other protect them from the incoming merrows. 

Where i need help:
I'm a bit afraid of making the final fight too stretched, or palyers covering the "pilot" feeling left out or isolated from the encounter.

As a baseline for the stone knight i took iron golem stats, but buffed it's HP from 210 to 260-ish and gave it 3 attacks, instead of 2. Fire absorbtion, on top of restoring HP will grant extra point of strength for each 5 fire damage it takes, untill it reaches 40 strength and will have to make saving throws or take force damage from overheat. That should be enough to have quick-ish and intense fight with dragon turtle.

Alternatively, i'd love to allow players to collectively control the stone knight, and channel their attacks and abilities through it (Yes, i do realise that this will be basically Power Rangers kaiju fight). But i'm inexpreinced and afraid to fumble the math. Just multiplying all the damage done by 2 could work, since there's 6 players and it amounts to 6 attacks, each dealing 1d6-1d10 damage, without counting in the spells they have up their sleeve. 

I could balance the encounter mid-fight. By either "enraging" the zombie dragon turtle, or making it breathe steam on the stone giant, making it regain HP and dealing extra damage, but again, i'm afraid of turning it into two tanks slugfest for 20 rounds. 

Any tips for balance?

I mean, are any of the players in this particular campaign interested in tokatsu/sentai type megazord fights? 

Capstone fights to me are the pinnacle of characters and their abilities and taking one character completely out of their sheet is something I'd never consider.  

What level are you having them fight the dragon turtle?  Is this the ancient dragon turtle from fizbans?  Some homebrew?

Players are up to basically anything, as long as it's not political intrigues. 

We have a fighter who started playing, basically yesterday(4 games total),  min-maxing~ish warlock, and rest are in the between. Everyone is currnetly lvl 4, and might get to lvl 5 before the whole dragon turtle adventure, since it's a bit further ahead. 
Dragon turtle itself is identical to https://www.dndbeyond.com/monsters/dragon-turtle. Eveything homebrewish about it is plot-related and doesn't affect the combat. 

My main concern is unbalanced fight and isolation of a player, who takes control over the stone giant. I'd love players to temporary scale-up PC's to dragon turtle, by them using stone giant. But afraid they will wipe the floor with poor thing. Or vice-versa.

Scaling up iron golem seems much easier to balance. 9d10 vs 3d12+4d8 seems more or less equall. At the same time multiplying damage dealt by players might yield completly unpredictable results. 6 turns of damage dealing, multiplied by two or even three, might deal far more, or far less than ~70 damage. 

First off, I love the idea of the mega fight with the party defending the control room. I may steal file that one for later use!

I would make the knight feel magical, and as such be able to channel any and all magical abilities of the player involved in controlling it. I would also have damage transfer back onto the pilot, and have it designed for a more powerful pilot - thus meaning that the players have to change out who's piloting it during the fight if they want to survive, which in turn gives everyone a chance to have a pop at the kaiju, and to channel their abilities through it.

As far as damage and HP is concerned, I would pick a comparable creature which would be a challenge for them, and then triple it's HP and triple its damage, have the knight triple their damage, and then have one third of the incomign damage hit them directly (effectively, you're makign them fight the creature one at a time until it has been defeated). The HP of the knight is "Plot", so you can have it mortally wound the turtle before being destroyed, or survive the fight, or whatever.

So, in practise: You have an enemy which does 2d6 damage normally, and you scale it up and call it a dragon turtle, for 6d6 damage. Then the players take 1/3 of that (approx 2d6 damage, though more likely to be average, which in turn allows you to plan it more readily) as synaptic backlash ("Your mind makes it real"). The players warhammer manifests on the knight through magic and they would deal 1d10 damage plus 2d8 for smite, so they get 3d10+6d8 smite damage, for big numbers and rolls which they will love!

AC is the only difficulty, but I feel like perhaps having them "manifest" as a magical spectre over the top of the stone knight (or something like that) would be a great way to justify their stats being used for the whole fight.

For the defenders, I would consider having a couiple of "turrets" to man which they can use if they find a way to keep the foes out - EG if they barricade the door, and the Merrow fail to break it, you don't want them to have a turn where they get to do nothing!

Returning damage would be overkill, since they have to clear out merrows and sea hag in the first place. It would be a pretty hard challange for their group and godzilla finally showing up would be "Boss music intensifies, chorus being to sing in latin" moment. 

My original plan was for a pilot to take either fire or psychic damage for each turn, but that would be mean and discouraging. But if there's say a pool of psychic damage, that could be shared each turn, that might work.

I was thinking about bottlenecking the merrows, but barricading the doors sounds even better. There will be a tribe of friendly dragonborns, taking cover in the fort from the magical mist and they could even help with barricades.

Would it be conceivable for all of the players to engage with the controls… simulate a Voltron situation?  

Maybe the fighter makes grapple checks using the augmented strength of the golem to wrestle with the monster…

Maybe the wizard gets to cast a souped up version of Shocking Grasp…

Maybe the rogue controls a hidden arm that extends out to deal sneak attack damage…

Maybe the barbarian summons a magical axe to slash at the monster…

So the players all get to act and Jet Jaguar the iron golem gets 4 or 5 turns to every one for Godzilla, but maybe give Godzilla some legendary actions to even it out.

Just remember, any story where Godzilla does not win is just silly fan fiction.  Godzilla always wins, or else it doesn’t count.