What did you think Obama meant with his "Fundamentally transform" stuff?

The same thing that Trump meant when he said that Mexico would pay for the wall. Something he wanted to do, and wanted his supporters to believe he was going to do, but that would inevitably crash into the limitations of the real world.

yeah, I mean, why let pesky things like who's actually in charge slow down your agenda, amirite?

You're not "rite," because you misunderstand who's actually in charge. Congress is actually in charge, as the Founders intended. Congress controls the budget, creates the federal government, and writes the laws that govern what it's supposed to do and how it's supposed to operate. The President is limited to implementing all that.

Congress doesn't act very much these days, which is why federal policy has a lot of inertia. Democratic Presidents can't make major changes to implement their agenda (which is why there's no carbon tax or cap and trade or binding climate treaty), and Republican Presidents can't make major changes to implement their agenda (which is why Trump has to mostly live with what the EPA is generally doing today. Oh, sure - everyone pretends like the changes that Presidents make within the contours of a statute that was passed five decades ago are significant - but nothing compared to the sea change of Congress actually passing a new piece of landmark legislation.

The fact remains - Congress made all the rules that shape the contours of the Federal government, and neither party has amassed enough of a majority to make major changes to those rules. Which is why the Federal government isn't especially responsive to the preferences of whoever just got elected.