Well, its a good question and since I've raced my 749R for an entire year and my racing partner has a 2007 R6, I can probably give you some good feedback.
The 2007-2009 R6 is pretty much the best supersport bike ever built. Its extremely light weight (368lb dry, off the factory floor) has good tunability for cheap (IE: exhaust, PC3, suspension etc) and they're cheap to buy and own.
The 2004 - 2006 Ducati 749R is arguably the best setup production Ducati superbike made. With the adjustable rake/trail, progressive shock, wheel base extendable swing arm (also on all 05+ models) Ohlins all the way around, slipper clutch and race derived gear ratio's. But, out of the box it weighs a metric ton compared to the R6, roughly 415lb's dry. It was also a very expensive bike originally, running in at $28,000 bux's, compared to its $9,000 rival.
I went into the 2009 race season with a bike I thought would last the entire season without much adjusting... I was wrong. The bike has thrown me curve ball after curve ball, all season long. From blown voltage regulators to oil pressure sensors and clutch failures, its been a long, arduous year mechanically. The upside is, due to the 749/999's very easy to access components, like clutches and suspension adjustments. From ride-height to wheel base, you can dick around with things until your blue in the face. Sometimes thats good, but other times, you just want a bike to get on and ride, regardless of the setup. I think this point is the biggest thing that separates the Ducati from its Japanese counter parts. Ducati: "Making Mechanics out of riders since 1968" and that's been my experience from this season of racing. Mind you, I do beat the living shit out of the bike, but so do all the other guys riding Japanese bikes.
With that being said, most people say: go with the Japanese bike because its cheaper and more reliable. Thats not necessarily true either... Japanese bike guys are stuck in a world of compactness. So when the bike does fail, working on it and determining the problem, comes down to a lot of work. I've seen TUNS of blown Japanese bikes this season, I've also seen people crash once and never come back to racing again because their bike is totaled. Ducati's do tend to crash better then Japanese bikes if you put on under-fairing sliders and low-side a lot. I've seen R6 engine blocks get cracked from simple 50mph low-sides, ya won't get that on a Ducati. I'd say the biggest reliability issue with Ducati's is the motor and even that is pretty rock solid for the first 5,000 miles of track use which is at least a few years for some people.
In the end, it comes down to the rider and his/her preference. I happen to like Ducati's because they're unique, the 749R is not cookie cutter and its taught me a lot about race setup because I learned all about geometry due the ease of adjustment and the ability to adjust so much. Good luck finding a ride-height adjuster on an R6, it doesn't exist. Good luck replacing the R6 shock, thats a weekend worth of work! The Duc's are easy to work with and very rewarding.
Ohh and yes, you can go just as quick on a well built 749R vs well built R6.
