I'd say go with the most interesting character. There are plenty of bad guys as the protagonist you just have to make them human so that your reader will sympathisize with their want and need.

I keep remembering the movie, Payback with Mel Gibson. He was 'bad guy' that just wanted the money that was owed to him. A lot of other nasty guys were making that a challenge for him.

I'm curious what the story would be like if Voldemort was the main character instead of Harry Potter....

What it comes down to is you do what works for you.