without being totally clear about your goals or application, I would suggest getting the axial mount 65mm 4 piston 2 pad brembos. they were on a bunch of bikes and can be found pretty cheap, throw on a set of radial master cylinders from any superbike/streetfighter/ high spec modern monster or hyper and you have a substantial upgrade from stock.
caliper example:
http://www.ebay.com/itm/Ducati-Monster-S4-Brembo-Brake-Calipers-65mm-S4-620-750-800-900-SBK-ST-/271836174377?hash=item3f4ab2d829&vxp=mtrI have an S2r 800 running the above set up and I feel its perfect for my track days. brake pads and levers are readily accessible and im not adding any unnecessary weight by going with overkill calipers.
Our bikes make like 80hp and weigh under 400lbs, we dont need massive brake power.