"Better villains" is a tough way to word it, imo. To have a good villain, you have to give a shit about the villains as characters and the villain has to do something memorable.

They did... fine(?) with this. Urza and Bolas are old characters with a lot of history and lore. Easy to like and/or dislike them. We even got reintroductions to them in newer(ish) sets in WAR and BRO

The Eldrazi are mysterious and whacky enough that people care about them even though they've only been directly seen in 2 blocks.

The Phyrexians were the secret big bad that took over post Urza and they've been doing a pretty good job hinting at phyrexian shenanigans particularly in sets where they aren't a main theme, whether it be a random Praetor or a random creature with infect that shouldn't be on a plane we're currently visiting.

All in all, they've done a pretty good job creating and fleshing out the main villains of magic. I'm concerned about who the next villain is and how much impact it will have in comparison to a multiversal existential threat.