Personally, I like Ganondorf more than Bowser for what I guess could be considered more shallow reasons. I like the variety of designs he's had over the years, particularly his Wind Waker incarnation with the twin swords. Whereas Bowser does have a clean aesthetic that has been refined over the years, Ganondorf has been more varied over the course of his incarnations in various media. Each Ganondorf is almost a distinct entity, compared to Bowser being one character across a myriad of games...And there's merit to Bowser being more "realized" and having more development over the years, certainly. But I rather like the idea that everyone can have their own favorite incarnation of Ganondorf. I'm also a sucker for the aesthetic of the Gerudo people and culture, so there's that.
The other reason I lean Ganon is that he's more threatening than Bowser as a villain. Bowser is imposing due to his size and spikes and fire breath, and even his ingenuity when it comes to inventions and plots to kidnap Peach/best Mario, but he isn't as menacing as Ganondorf. He's a warlock, he wields a piece of the Triforce, he's got a big honkin' sword, he turns into a giant monster...I dunno, I think it just comes down to me thinking he's "cooler" than Bowser.
