Questioner
Goku vs Elders and Emperor. If Goku loses, then Beerus comes in
Will Wight
Based on what we've seen from Dragon Ball Super recently, even the creators of the show have no idea what power levels mean. We have Super Saiyan Trunks fighting evenly with Super Saiyan Blue Goku and Vegeta, which makes NO sense. Plus Goku gets pricked by a poison needle during his fight with alt-universe Freeza, which seems to violate canon in like three different ways.
This effectively means that recent events have suggested that Goku isn't really THAT strong.
Anyway, disregarding recent events that retcon Goku's strength and using our own reasonable standard of his power level...
1.) Goku vs. the Emperor and the Elders
Let's assume, first of all, that Goku doesn't just blow up the planet and cause everyone to lose.
...although, now that I'm thinking about it, that would be the worst thing he could do. Without the existence of Intent-wielding humans, the Elders would be free of their confines, and they would escape into their true forms. At which point they would unmake Goku at a conceptual level. The Emperor would still die, but his team would win the battle.
However, assuming Goku doesn't destroy the planet, he would tear apart the Emperor and about half the Great Elders. Any of them that work physically: Nakothi, Othaghor, Kthanikahr. He'd blow up their minions, fly in, and tear them to pieces.
But against the more metaphysical Great Elders--Urg'naut, Tharlos, Ach'magut--I suspect he'd have his mind devoured or his soul ripped out or something. As far as I can tell, he has no ability to resist powers like that.
And I can't imagine Kelarac wouldn't be able to outwit Goku.
2.) Beerus vs. Elder Empire
It depends on how Beerus' powers as the God of Destruction work in a universe that isn't his own.
If he can still unmake entities the way that he unmade Zamasu, then he would certainly win. The Great Elders actually can't be unmade this way, so they would re-form in the void and attack some other, random world, but that's not enough to invalidate Beerus' victory.
However, if he's relying on sheer strength and not his authority as the Destroyer, then he has the same result as Goku. He might be able to resist one or two of the metaphysical Elders, because presumably gods have some kind of spiritual/mental fortitude, but all of them working together could probably defeat him.
Whis, on the other hand, likely just wins. I can't see the Elders beating him physically or metaphysically.
Questioner
Woah. I thought you would say Goku would lose immediately.
How about Naruto. Him vs Emperor.
And vs physical Elders, not metaphysical.
Use Sage of Six Paths Naruto
Will Wight
I've seen nothing in the series to suggest that Naruto could ever compete on Goku's level, so I'd think Naruto loses to everybody.
Now, that's assuming he walks in and tries to fight Nakothi (or whoever) on his own. As part of a team, like for instance one of the Emperor's teams that actually went against the Great Elders, I think he'd be a huge asset. And a big threat to the Elders.
Naruto vs. the Emperor would be the closest fight. Naruto's powers are more physically threatening than the Emperor's, since he can use blasts of destruction and the Emperor can't. However, the Emperor's powers of Intent can also counter a lot of what Naruto's capable of doing--the Emperor would have superior elemental control to Naruto, for instance, and he could likely make Naruto's clothes shrivel up and start strangling him. He effectively controls the whole world around him.
So the incompatibility of powers makes this a little bit of an awkward matchup, but I'd PROBABLY give it slightly to Naruto. 51-49. The Emperor is smarter and older and wiser, but Naruto has many crazy powers in one body.