i believe the quickest way to get from TPE to PVG is by flying Far Eastern Air via Jeju in Korea. Time en route is about 4 hours and if you take flight EF718 (15:25 departure from TPE), you can make it in about 3 hours and 35 minutes (7 PM arrival in PVG).

refer to the following link for timetable (unfortunately it's all in Chinese but look for the section with "桃園 - 上海".

"thousands of taiwanese" fly through HKG because there's more flexbility with the schedule and more mainland destinations to choose from, not because it is faster. in fact, it is often slower because the skies are so congested. and, for the shanghai route in particular, HKG<=>PVG flights do not take the most direct route. i believe most of the time, the flights take the coastal route, which adds quite a bit to the distance/travel time.

in general, i find the HKG<=>PVG route can be a bit more pleasant than what it is now, with the frequent delays, flight restrictions, etc.