I guess it's cliche to talk about how Bowser isn't really the villain, but think about it. Bowser never kills anybody from the Mushroom Kingdom. Mario kills thousands of Koopa civilians in every game.
Bowser's villainous plans involve nonlethal surgical strikes against a known aggressive military power. His demands and further plans always boil down to "stop hoarding all the resources in the universe, you dicks!"
For example, here's one of Bowser's evil military plans:
"President Bowser! We've finally completed our armada of flying battleships! We can finally get vengeance for the tens of thousands of innocents murdered by those Toadies!"
"Yeah, sir, let's glass 'em!"
"No! If we kill them, we become them! Instead, we will perform a nonlethal surgical strike to capture their main military fortress and their leaders. Then we will negotiate for reparations and peace!"
"Snf ... you're my hero, sir!"
"Thank you! Now, man the nonlethal stasis beam cannons!"
Then, of course,the interdimensional horror that is Mario comes along and murders everyone. And the Mushroom kingdom releases another piece of propaganda about the evil "King" Bowser.
This propaganda isn't even vaguely believable. Princess Toadstool is some kind of willowy blonde lady? She's a mushroom. She's princess of her people. She looks like them. And Bowser? Thirty feet tall and breathing fire? Yaright, we believe that, Mario. He's just a turtle with a skin condition.
You're the only one that changes size and breathes fire, you pandimensional horror. The nuclear weapons program of the Mushroom Kingdom.
The only real question is why the people of Koopa Democracy keep electing Bowser if he's always losing to the Mushroom Kingdom. The answer is actually that Bowser is a really great leader. Think about it.
1) He always loses to the Mushroom Kingdom, but when he does so he lures the mass-murdering Mushroom Kingdom strike teams into some crazy death trap far away from Koopa civilians. And then he faces Mario head-on so no more of his men have to die.
2) The times someone else comes to power it tends to be an interdimensional godling with an indecipherable accent and a lust for murder. Sounds like they all come from the same place - Mario's world.
3) He's a really great peacetime ruler. First, he rebuilds everything between wars. Not just military armadas, but theaters and factories and playgrounds. Second, his people are so wealthy that even the random soldiers can't be bothered to grab the money, clothes, and food that litter the landscape.
It's a laugh seeing Mario smash what we loosely refer to as its "head" into brick walls just on the off chance we accidentally dropped a penny inside. Well, until it suddenly starts flashing and killing us while moving at mach speed.
Hell, in a world where that sort of creature exists and is on the leash of your worst enemy, wouldn't you keep electing the guy that keeps it out of your towns and cities? The guy who is willing to give up on military objectives just to protect his own civilians?
This is a real stand-up turtle.
Villain my ass.