I have both pickups, the Juggernaut and the Miracle Man.
In many ways, the Juggernaut is simply the "better" pickup: it's more refined, tighter, crunchier. It has a better clean sound, and its many upper mids make it sit better in the mix. Still, while my head says Jugg, my heart prefers the Miracle Man. It just sounds bigger, more brash and has more attitude than the somewhat stiff and controlled Juggernaut.
It's really like Periphery as opposed to Zakk Wylde in his best days. One can be characterised as complex, progressive, with a busy mix and lots of details, the other is about drinking beer, heavy metal and kick-ass riffing.
On a more neutral note, I think the Miracle Man does have better harmonics for soloing and its lead tones just sound a bit better than the Juggernaut's (which aren't bad at all!).
I should also add that I use both in mahogany body/set neck guitars.