I've been running MtAW for a couple of years now, its the most popular game line in my group. What I normally do to balance mixed genre games is placed in the design of my setting. Most supernats have a form of social hindrance when using their powers such as the masquerade for vampire and the paradox for mage (not to mention "keepers" for changeling and Lunacy for werewolves.) This social challange becomes the key ingredient for me when I run mixed genre NWOD.
Here's an example: A werewolf, a vampire, and a mage go into a crowded night club, all three player's decide to use a power. The vampire seduces a women in order to feed for the night. Since Majesty (or dominate, auspex, and obfuscate, etc.) doesn't gather much attention from mortals without an ability to see mystical powers, there's no real danger to the masquerade. The werewolf at the same time in the club is attacked by a spirit of murder and defends himself with a gift. If this gift is something that even a no exp mortal could notice than lunacy kicks in and the mortal literally makes up a fictitious story as to what he'd just witnessed. Now the mage, the mage opted to teleport into the bar's restroom in order to get passed (insert plot device.) Since teleportation is vulgar even on the best of days a paradox roll is made.
Firstly, and this is where setting design really levels the playing field, establish your paradox dice pool. If mage really isn't your thing than don't run it until you get comfortable with the paradox mechanic because it's what balances the game lines. Its Half gnosis rounded up contested against half the player's wisdom rounded down, + the gauntlet rating of the night club's spirit world + two for any sleeper in the bathroom who noticed anything "strange." I use strange loosely because the more Over Powered the mage in my setting the more observant sleeper's tend to be.
So despite the over powered nature of mage, the consequences of these three supernats go something like this, The weakest in terms of power, the Vampire, has a great night and a full stomach for intelligently using his discipline. The Werewolf, the second place runner in power level, may attract some unwanted attention of supernats in the bar since whatever power they used to cause lunacy typically causes a bit of a scene and the vampire sitting across the room now knows theirs a wolf in his sheep and may chose to tell the prince. The over powered mage however, could be dead, if the bathroom had three sleepers in it (+6), and the night club had state of the art security (which increases the gauntlet rating to about 3 or 4), and the player only rolled one success to stop the paradox with a 3 Gnosis (-1 your dice pool of 11) than your rolling 10 dice, with one out of three odds for success, that's three paradox for using recklessly using an OP power congrats to your player he gets a bedlam (a severe derangement that can't be mystically removed) for as long as you feel is appropriate. That's assuming you don't roll high or low on the roll. Rolling 5 would mean the player takes resistant aggravated damage equal to his total number of accumulated paradox points this scene.
So to sum up, in mixed genre, the socioeconomics of a setting become really important. You've got to plan out your setting's Shadow for both werewolf and mage to determine the spirit gauntlet as well as an vital social aspect of werewolf deciding how much hell the wolves catch learning new gifts and possibly use the shadow as an advantage over vampires, sin-eaters, Promethean, and mortal. Also, what kind of prince, if any, is in charge of what is considered "a breach" in the masquerade. Bear in mind that in addition to paradox, mages also have to deal with the Heirarch of any given city who typically punish reckless mages since invoking paradox damages the spirit world increasing the gauntlet rating in consequent areas.
I hope this was of any value.