Speed was never stated to be equalized. :/
Speed unequalized:
Mario speedblitzes Link to oblivion, and one-shots him, too.
Speed equalized:
Mario is literally over a thousand times stronger... High-end High 4-C against Link's baseline. Even with upgrades, nothing of his can multiply his durability over a thousand times. So, the second Mario's breath brushes against Link, he's dead.
Now, we just need to talk about whether or not his breath would be able to catch Link.
Talking of hax, yes, Link has more to offer. But Mario resists all of his elemental manipulation, plus more. His precognition is useless, so he has no idea of what Mario will be using, and with so many power-ups, the plumber is actually pretty unpredictable. Furthermore, Link has never resisted possession, so all Mario needs to do is knock his hat off his head--not hard, and Link has never resisted transmutation on Mario's level. Mario's transmutation works on Bowser, who is also over a thousand times stronger than Link. He may resist weaker transmutation, but nothing on Mario's level, so if he gets hit, he's turning to gold, period. Shoot, if Mario just dons the Vanish Cap, he can turn intangible for 25 seconds; much more than enough time to run over and hit Link once. And while Link has the Lens of Truth, there's also no telling if he would flash it right over Mario before he gets hit, or if he'd even think to use it right away. Links exploits things first; then, he uses that thing's weakness. But there would be no exploitation if Mario just up and disappears without a trace. Both have time stop, so that's a null point, too. From there, there isn't much else Link has that can get by Mario's advantages, and most of his hax Mario has encountered before. He may not resist them, but he's well aware of how to deal with them, while Link hasn't faced too much that's akin to Mario. Furthermore, Mario's time travel is way superior to Link's, so he has no advantage in that department, either.
I'd say Mario takes this. And really easily.