While I do believe the Board of Regents is an antiquated system (which seems to be why the Speaker likes it, according to his quote in the article), I'm even less in favor of having governors in charge of education in the state. At least the Regents have tried to convince the governor of the need for more equitable distribution of funding, and at least they accept the counsel of District Superintendents statewide. Make the governor the commissioner's puppet master, and not only will we see major swings in education policy (and a new commissioner) every time there's a new governor, but also we will see education truly politicized, without the meager checks and balances that currently exist.
Gubernatorial control of education is happening all over, not just in NYS. Deval Patrick in MA made a grab in 2008, establishing a Secretary of Education cabinet post over which he had control. Other states are in a power struggle similar to the one that's about to happen here. This map is from 2009 and shows where governors had full control back then. But more important is this chart, which indicates that governors in many states with boards of education (like our Regents) often have full control over who gets appointed to those boards.
It's good to be the king. Not so good for Commissioner King, who is on his way to DC. What do you want to see in the next Commissioner? Something like this?