I've been thinking about this and usually I'd go with the cliché, well, obvious choice - Ganondorf. However, I've been thinking about the concept of a new villain and sometimes it can be hard to introduce a new villain and have it compete with the likes of Ganon and his legacy, but if done right I think it could breath new life into the series.
For one, a new villain doesn't have to rely on old staples in the series; it can take a different route, and I feel that's where we will have something fresh. Of course we've had a fair share of new villains being introduced, but they don't have that long term effect, nor do you ever feel like they're something more outside of that game. Take Zant and Ghirahim for example, both were great villains in their own ways, but outside of their respective games they're basically nothing. What if Nintendo were to create a new main villain and by "main" I'm talking long term as they will make several key appearances down the line. I guess one big problem is that it may be hard to just retcon in a new villain especially in the middle of certain eras we already know of in the Zelda timeline. So for this to be executed right, they'd have to find a spot to introduce said villain that isn't contradictory to the constraints of the timeline and so that it makes sense.
What traits should this new villain have then? Well it's hard for me to just create a new villain on the spot, that's Nintendo's job; however, I do have a few ideas in mind. First off I think they should break away from two current trends for: out of the ordinary villains and sub/main villains. It seems like a reoccurring theme now to have one borderline crazy villain serving a higher power. Make this villain distinctly the greatest threat. Also, break away from Ganondorf and his traits, what would be the point of making Ganondorf 2.0? I would love to see a young villain rising to power, maybe the heir to the throne of evil and one that is stronger than anything we've ever witnessed. This also allows for character growth. We can see this villain transform throughout the game from a careless, rather naive, power hungry man/woman to eventually becoming a more clever, more tactical villain - and maybe this villain will also go down the route of going absolutely mad with power, who knows?