I think the vehicle is operating as designed. The RPM's on the V6 don't drop immediately, and if you shift quickly, the RPM's are right where they need to be for a smooth, almost unfelt shift.
In other words, if you bring the revs up to around 5500 - 6500, and don't lollygag with the shift, the motor by it's slower rpm reduction is working in your favor to match the gear/motor rpm's. Does that make sense?
I had the same experience just before I stored my car this year. There's absolutley nothing wrong with my vehicle. Making a quick, complete, and smooth shift at high rpm's, will set you up for a very well matched gear and rpm shift.
Mustang base coupe, V6, manual transmission, Red Candy tint, performance package.
Upgrades: DSS aluminum driveshaft, BMR LCA's, Yukon 3.73 gears, MGW shifter.
Displaying 3.7 fender badges is like telling everyone your wife is "office hot."