If the bike is tuned properly for low speed running, you should be able to let it coast down nearly to idle speed. I think the sad fact is that a lot of tuners don't spend any time on the range between idle and 2000 rpm, so even a canned map or a full tune may still have the same settings the stock bike had. My advice, find a good professional tuner and tell him you want it tuned from idle up for the smoothest performance. Instead of just looking at those wide open throttle charts used for bragging rights, look at the charts for part throttle operation at various rpms.
Btw, my older bike had the same issues you guys are complaining about on your late models, both stock and after a supposed tune by the local Power Commander Master Tuning Center (what a joke that was). After I spent a lot of trial and error time tweaking the low speed fuel settings, I can now putt around the neighborhood at 1500 rpm with nary a stumble or grumble, and coast down in top gear to less than 1500 rpm also with nary a stumble. In other words, it can be done.
Jerry