The Subspace Emissary was interesting for its time, and I remember loving it as a kid. One thing I think didn't sit well with me was the fact that literally nobody talked and the plot just seemed...weird, and actually distant. It was just kinda like, "hey these characters showed up", but why did everyone happen to be in this generic overworld that didn't have a specific ounce of "Nintendo" to it?
If they did another mode like that, I really think it shoudl just be named "Story Mode" and I'm not really sure if they could get away with not doing voice acting for it this time. Not every character would need to be voiced (Mario characters, Link, etc...) but it would be awkward, to me anyway, to have the characters who DO speak not really be the mainline Nintendo characters. Characters that speak/have spoken in their source games would be Shulk, Lucina, Robin, Snake, Cloud (probably Japanese), Ryu, Bayonetta, and then the other characters kinda either make noises or would have to look into cartoon/anime...I would love Dedede from Kirby Right Back At Ya!, as that voice is honestly hilarious. But it would unfortunately not lead to an entirely compelling story in that regard.
My biggest issue with NOT doing a "Story Mode" is just the scope of this game. This is basically Super Smash Bros.: Infinity War, or at least a gaming equivalent. While we don't have heavy hitters like Master Chief, Kratos, or Nathan Drake (which, personally, I think would be both hilarious AND awesome) this is basically as Sakurai said, "The biggest crossover event in gaming history". This has never happened before and may never happen again. A story involving that sort of magnitude would be amazing.
I've kind of considered a few different scenes of what they could do, such as pairing Mario and Sonic, or even Megaman together, and then maybe the Princesses. Or maybe the Princesses play some sort of part as a plot device ala Kingdom hearts, (though I would rather see them doing badass things together), but the whole idea of characters meeting each other for the first time (like that idea of Simon Belmont and Bayonetta) is just too good to pass up in my humble opinion.
The thing is, do I want a quality story mode to take up the time of development? Or do I want for characters, items, stages, and other content? I'd take the latter.
Although, one thing I would be down for is if the story mode was released in stages or something as DLC down the line.