Most definitely Dio. In fact probably all the main villains minus Diavolo were just far more interesting characters and villains. Freeza is a cool villain, but he's very generic and unfortunately is stuck in that very blatant shounen style of villains seen at the time.
Dio Brand not only has a backstory, but has characterization to him and there's a lot more material on Dio beyond what's seen in the likes of Phantom Blood and Stardust Crusaders. Dio Brand was a character that was meant to be more than just the generic villain that has to be stopped. He's a person who is actually depth, something that...let's be honest, a good number of villains in DBZ don't have.
Dio Brand is essentially everything that Freeza has, badass, powerful, suave but with so much more added to him as well. This really does make him the more interesting and better villain.
Araki has a tendency to make really good characters. Even someone like Part 4's Yoshikage Kira, who by all means would be the most generic antagonist ever, is given depth and characterization that has made him practically not only a fan favorite villain of the series, but a fan favorite character as well.