Advantage of flying: The pure travel time is obviously lot shorter, but if you've get to PVG (SHA is better especially when you take the train from Hongqiao anyway) and in PEK need to get back into the city/South area, you'll easily take more time, even on a fully on-time flight.

Sure, you get to relax in the lounge at the airport, and while they're ok for 30 minutes wait (which you'll have, unless you want to to cut things really extremely close) it's not the best experience either.

So, for a train departure, I'd plan to arrive 30min prior to departure, for a flight, 1.5hrs (each giving 30min extra time - yes, with the train it's a bit less than 30min..) - that's one hour to add to the flight time (assuming departure from SHA)

Then, in PEK, if you've luggage, you'll have to wait a bit, and even if not, it will take a bit time to get landside. Then it's the train into the city.. another 30-60min in total to add to exit the Airport Express.. then you're about as central/down town as you're when you exit your HSR train.

So, that means you're about 1hr faster by aircraft if all on time vs. taking the HSR. Personally I like the HSR service, especially the one that only stops once (at Nanjing) and then goes direct all the way to Beijing.