Urza does have a lot going in his favor in comparison to other mono-colored decks, notably getting to actually play counterspells and Rhystic Study
Here's some of Wizards' explanation for the banning: The last turn-three deck that remained was Dredge...Dredge is not known for being fun to have around
Putting the imagery on cards that are also powerful creates a pretty awkward situation
Yes, this came at the expense of Limited play, but if that was the cost of staying in business, that's what they had to do
So on first glance you're right, Mishra seems like an awful choice to pick as a commander, but there's something really neat to be reaped here if you look at the ability really close
The decks span four of the most popular archetypes: Slivers, Eldrazi, Enchantress and Superfriends