I bought my GT-1000 new in '07 with the DP kit installed, so I haven't got a 'stock baseline' for comparison. As equipped, the fuel injection had a mild hesitation at 3K......but only until warmed-up. After that 'Lil Miss Duckie was a hooligan's dream.
After the dealer's 7500-mile service, it turned into a full-time hesitation. I was NOT happy. Each time it was worked on the glitch got worse, the problematic RPM range increased, and the fuel mileage dropped.
I finally got pissed-off enough to have them install the stock ECU and Oh-Two sensor, until Ducati was ready to provide another DP ECU under warranty. Fueling smoothness improved greatly, and highway mileage was consistently over 58 MPG, with high 40's in town. I lost some of the SNAP! throttle response, and She ran noticeably hotter, but no real ill effects.
When the replacement ECU arrived, almost all of the SNAP returned, the heat went back down, and fuel mileage is still high-40's in town. I haven't had the chance to highway for a full tank since, but if I can hit 50+ MPG in the open I'd be happy.
Hope this provides a little insight.
*QuACK*