I know a lot of people would prefer for K. Rool to stay a villain, but I think Bowser's short misadventures as a hero or begrudgingly working with Mario helped him get further fleshed out as a character, and I think more people enjoyed him because of it. Not to mention, in the many games that the devs took a chance and made another non-Bowser villain, Bowser still showed up as either a 3rd party villain or even an ally.
Think of it this way:
King K. Rool could have done the same thing while bringing in the Tiki's and Snowmads. Having him be main villain only, that means he has to be on the bench anytime someone wants to bring something new to Donkey Kong. Where as you see a score of non-Bowser Mario villains with Bowser still remaining completely relevant throughout, instead of not getting a game in years. Not saying he has to do a Heel Face Turn and be a full time ally of the Kongs, he'd hate that, but you need to consider what role he would take if another villain showed up, as opposed to simply not being present at all like he has been.
Beggars can't be choosers, if we get K. Rool in another DK game.
He works great as a diabolical, if not bumbling villain, but if he was a little more dynamic and varied he could elbow his way into more games.
Edit: King Dedede does the same thing as well, having been playable even in Kirby's most recent game (scratch that, one of his most recent games) in Triple Deluxe. Sure, he's more of an anti-hero than a villain at this point and has been since Kirby first started, but it helped Dedede become more distinctive. Maybe I'm wrong and King K. Rool simply can't be seen as anything but the main villain like Ganondorf, but I think there's wiggle room there.