Yes I'm sure it'd be a design challenge. In mods/hacks of the games you can play as the boss character relatively normal to how your accustomed to playing characters. I'll link you to the Master Hand glitch to get an idea. I'd presume boss characters would be controlled like this. I propose an additional "guard" feature that heavily minimizes damage to barely anything at the cost of being unable to action your attacks while doing it. This would give this mode some needed depth and allow for players with more skill to really push the limit of what the mode is capable of.
https://www.ssbwiki.com/Master_Hand_glitch#Controls
Then there's the map size and I'd assume there'd be special stages for the boss fights like there are already and that players would be locked to these choices with extremely limited special smash features (or none at all) and exclusively tied to stamina matches. Then I'd also think either these stages would have to be bigger than they already are in order to account for 2 boss characters fighting on the screen OR the game would simply do that when that happened and keep the original size ratios when it's just a single boss character on the screen.
I'm a fan of player choice and when I see the potential I advocate for it. I feel that if we're to implement boss rush mode it's best to take the mode to it's absolute limit of potential play in order to maximize the results of the development. Might as well if you're already investing resources into it.
Squad Strike mode suffered from this lack of vision. Limiting character select to just 3 and 5 exclusively? Why? What was the point of that? That just minimizes the limit of play. That's literally all that decision produced; less player choice. Also no ability to swap characters without losing the stock? Need a button for it? Easy just have it tied to a simultaneous R3 + L3 input
(don't get me started on the GameCube controlled because I have some strong opinions on Nintendo's weird relationship with that beautiful controller in desperate need of a modern update) and if it's players constantly shifting characters then put a cooldown on it that way it nips that potential problem in the bud and also further emphasizes the importance of rotation order to the mode.
They are but the big green Smash 4 custom one I'm suggesting be allocated to either would amplify the differences yet again. That's more or less why I'm suggesting it. I actually have an effort post I'm working on of Smash 4/Brawl content that could be imported/reappropriated for a potential Smash Ultimate DX. Suffice to say that utilizing those customs in one way or another by either giving them to appropriate existing characters or creating characters like Ninten for the sole purpose of repurposing some of these moves is the aim of this particular advocacy.
Moving on to other topics brought up here...
Two things! In regards to Megaman. First off I hate when characters' jabs are tied to their Forward-Tilts in order to make them "work" in Smash's currently outdated stick design. There's no reason a jab can't simply be walkable and a character with one of these walkable jabs be given a unique Forward-Tilt other than Smash's insistence on keeping to a design that's simply outdated at this point. More of my opinions in general on all of that in my signature in regards to moveset expansion ideas.
Next my proposal for Megaman to regain his custom moves would be a Shield-Special Weapon Wheel.
Press Shield-Special a Weapon Wheel will appear around Megaman. Megaman is now standing still and cannot do anything until he either actions out of it or cancels it by shielding/crouching/jumping similar to how Hero acts when he's shuffling through his spell menu. Each weapon on the wheel will be his old customs from Smash 4. You can select one by holding the control stick in its direction and by pressing jab (A) you'll simply equip the weapon without doing anything but if you press special (B) you'll immediately attack the selected weapon simultaneously as you equip. When a weapon is equipped it is assigned to your Neutral-Special whether it was one in Smash 4 or not. When you lose a stock your Neutral-Special is reset back to Metal Blade by default.
Under my Shield-Special design philosophy like all other Shield-Specials, Megaman wouldn't be able to do this in the air and he'd also be completely vulnerable while he was doing it on the ground being unable to shield without suffering a bit of endlag of the move and canceling the weapon wheel itself.
On the topic of Nintendo regaining Rare IP for some reason. Oh no. Why would anyone ever want that? Nintendo notoriously sit on their IP and even IP they consistently work on are in a pitiful state like Pokemon and even freaking Donkey Kong is getting neglected as of lately. Nintendo wouldn't know what to even do with the Rare IP if they had it. They were simply hosts and of course we all fondly remember Rare's time with Nintendo but so long as Banjo stays in Smash and other Rare veterans get that chance too then it'll have literally all worked out for the best. Every Rare IP has a better shot under Microsoft. Perfect Dark is getting a new game and the Killer Intinsnct reboot was sick as **** and heavily supported despite being by all accounts a budget title.
For Banjo and Kazooie I see 4 potential developers. Rare themselves which would be fine I guess. I hope they'd go for a game in the series that plays more traditionally while also expanding upon that tradition similar to how Crash 4 worked. Then there's Doublefine who have proven themselves capable of making great 3D platformers though I think their skills would be better suited for a Conker game. Finally Toys for Bob could definitely do it too based on their work with the Crash and Spyro series and I'd love to see what they'd do. Last they could try to get the old team back together by outsourcing either the entire development or a significant fraction of it to Playtonic. Any one of these outcomes would be drastically better than Nintendo definitely sitting and doing nothing with the IP.