Actually, I've found that the MC's side is the MOST IMPORTANT side of the hack. On my (stalled) hack, I've only hacked the MC's ruleset: agenda, principles, moves, threats, fronts, etc.
Think about it this way: the MC's rules, as a single system, do more to shape the way the game is played than anything else. Not the playbooks or even the basic moves. It's the way the MC sets up the game, the moves he uses all the time, the structure of the challenges--hell, even the basic goals of the game!
Not to say that much will be changed, but I found that color and inspiration are as much a part of hacks as mechanics. BUT if you want to look at a couple existing examples side by side....
Apocalypse World has threats, picked form a menu, each with a unique impulse that is different for each type of threat, but common moves for threat types. Threats are organized thematically in fronts as large or small as needed. Fronts--not threats--have dark futures. Threats just help bring that to fruition. Side note: I like this system the best. It seems the most organic. But that's just me.
Monster of the Week has a single monster every week, necessarily with some custom moves. That one monster, plus some SPECIFIC other threats (bystanders, landscapes, etc.) makes up the front for the week. You "solve" the front and move on to a new one. Then, the arc of the longer story is another, slow-burn sort of front, living in the background. This makes for a totally different feel to the game.
Monsterhearts has no formal "fronts" system except for the unique way threats are created. Impulses, moves, and leverage are all chosen separately, creating a mix of different options. There's no thematic groupings, since threats take up more fictional space in the smaller world of school.
So hacking the MC's side doesn't have to be just moves. Changing the agenda and/or principles (take a look at Monsterhearts again for an awesomely different set of those) really changes the focus. And changing the threat impulses totally changes the challenges that the PC's will face.