That seems like a mighty straw man. He never said he disagreed with the permit process. He simply disagrees with the idea that these companies have been able to park illegally with no consequence for years and instead of just writing them tickets, as the city would do for a normal person, they decide to give them permits to prevent them from having to break the law hundreds of times a day.
I expect there to be a fee associated with these permits.
What if the permits are issued with a retroactive start date (and proportionately large initial issuance fee)? Perhaps one that extends back to when each company started stopping in city bus stops? How would you feel about that?