I can relate to every one of your observations, except the clunky tranny...my 2009 1700 had a pretty smooth tranny (to the best of my recollection).
1) Stock Seat Sucks...First thing I did was get a Mustang.
2) Stock Throttle Actuation Sucks...Second thing I did was get a reprofiled/recammed throttle tube from RACNRAY (search this site!) It smooths out the throttle, improves low speed control, and brings on the power band sooner with less wrist action...Major Improvement!
3) Drive Belt is Potentially Noisy if not adjusted to proper tension and alignment (simple fix).
4) Stock ECU Sucks...The stock A/F ratio is way too lean and it retards the timing as soon as the engine is warm...then you have a significant drop in power.
If I still had the bike the next thing on my list would have been the IVAN's ECU reflash. It addresses the timing issues and a multitude of other adjustments to make the bike perform the way it should have from the factory! These bikes are also known for generating prodigious amounts of heat and enriching the A/F ratio with the ECU reflash should help in this regard.
5) Some of the roughness you experienced might be related to the Ignition Wiring Harness Recall...(search this site). The wiring harness under the ignition switch/tank can get worn and cause shorting or intermittent wiring issues.
Oh, and if it has been sitting for any period of time, check each and every coolant connection and clamp
...you will need to remove the tank to do so, but believe me, it will save you a lot of grief...
Other than those few issues
, it was actually a pretty good bike...