I'm nicking u/PWNDdotcom's idea and hchoosing a boss from every series
Mario: That dragon from Mario Odyssey would be dope.
DK: One of the Snowmads, I haven't played much of Tropical Freeze.
Zelda: A BOTW boss I guess?
Metroid: Haven't really played Metroid so I'll just say Kraid.
Yoshi: Baby Bowser, the giant version.
Kirby: Whispy Woods, obviously. Or Marx/Galacta Knight (even though he's a Meta costume)
Star Fox: Andross (the monkey one, though he may be intruding on Master Hand's fight style. I guess General Scales would be a cool replacement, or an Aparoid)
Pokemon: Giovanni. He'd fight like pokemon trainer, sending out several pokemon that you have to defeat individually.
Earthbound: I haven't played too much of this game, so the only thing I really know is Porky.
F-Zero:...
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...
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Black Shadow?
Ice Climber: Oh man this was a bad idea. I guess it would be cool to have a Boss Battle where you ascend the mountain instead of fight something.
Fire Emblem: Ashera from Radiant Dawn, or Dheginsea the dragon king (i misspelled that)
Game and Watch: Oh man this was a REALLY bad idea. The octopus?
Kid Icarus: The Great Sacred Treasure, or a really cool fight with the Chariot Master.
WarioWare: DANGIT WHY DID I TRY THIS. I guess it would be cool to have to play microgames or die.
Metal Gear Solid: Senator Armstrong. I know he's technically from Rising, but do it anyways.
Sanic: Dahkta Aggman
Pikmin: Literally anything.
R.O.B. : AUGH WHY DID I EVEN TRY THIS. It would be really interesting to show up as an amiibo, and have to fight a real-life R.O.B. in the real world.
Animal Crossing: This was an awful idea. I guess you could fight against Tom Nook? We all know he's the best villain in gaming.
Mega Man: DOCTOR WIWY
Wii Fit: Fight a fucking giant Wii Balance Board. Get fit or get out.
Punch Out: Mr. Sandman. Some people might say King Hippo, but nobody likes him. Sandman is awesome.
Mii: Miitopia's final boss, using a random mii from your system (i want this because I have a Phil Swift mii, and that sounds like the best thing.)
Pac-Man: Toc-Man
Xenoblade: ... I haven't actually played this series. All I know about it is that the final boss is stupid and Metal Head exists. There's probably something in XB2 that could work.
Duck Hunt: Like the WarioWare and Ice Climbers ideas, have it be more of a minigame killing every duck or dying.
Street Fighter: Akuma or M. Bison. Finally, an easy one.
Final Fantasy: Chaos from FF1.
Bayonetta: Uh... Fortitudo?
Splatoon: That toaster thing.