The Martian mothership in Metal Slug 2. Unexpected, but a fun twist, and a hilarious ending (Unless you're General Morden or his army).

I think Blue in original Pokemon was a badazz mind fck final boss,

Lance wasn't too bad either in gold/silver/crystal

Malos in Xenoblade 2 Torna the Golden Country.

Probably has the coolest background set pieces that are mechanically important during the battle while you get also a though fight out of it ...
And yes, followed up by its famous heart breaking ending which is still one of the best sequence of event you could witness in a video game.

Also I'm surprised(or not) that it hasn't been brought around but Dark Bowser in Mario & Luigi Bowser's Inside Story is still the best climatic final battle in any Mario game in my opinion. Caps off a great trilogy and we get peak Bowser moments too

Also Imma gonna add the Dream Star from Kirby Planet Robobot. It's quite the gameplay change from a 2D sidescroller action game to a shoot 'em up that weirdly doesn't feel jaring because of it's scope and incredible music on display. It's a TRIP !

Last but not least, the final boss of Bravely Default which is the culmination of some would say a strange and complicated journey to one of the best final bosses in the JRPG genre too with none other than Serpent Eating the Ground to cap off an incredible music experience. 

Jubilee in Bayonetta 1. Platinum def saw DMC4's big statue fight and said we can do that but better. I love DMC4 but yeah that fight was kinda ass. Jubilee is fun and more creative. Too many games when a boss is building-sized, you just stand on a platform and avoid long slow sweeping arm attacks until the arm or whatever stops for a few seconds and you mash on it. This trope goes back to the 16-bit era. Even on Genesis with games like Mazin Saga Mutant Fighter. Even Astral Chain did this..ugh. For as much as I loved it. Soulstice made this error. So yeah Jubilee was fun and took a different approach.

Oh dear, how could I forgot the most epic of all?

That was a pretty scary Bowser, but the beta design was even scarier.

Warhammer Fire Warrior had the hardest and best boss I ever fought. It was a Chaos Demon!

Icon of Sin in Doom 2, especially because of the darkly hilarious easter egg.

Nah, that beta looks like a Moomin

Dammit I can't unsee that. XD

Also another great Bowser fight is at the end of Super Mario Bros. 3, even though it makes Bowser look like an idiot when he crashes through the floor and into the pit below.