When I have flown through PEK, it was about 3 hours for the connection after clearing customs, plus another hour or so for the flight, and then around an hour from the Nanjing airport to hotel. So four hours for a train ride (+20 minute subway ride from train station to hotel) does not sound all that bad. But, if it takes a long time to get to the hotel, that could cause issues. (How long does it take to get from airport to train station?) However, since it looks like a trek, this will probably be in the category of "only do when I really want to ride the rails" category.

Shanghai seems more valuable. It opens up a lot more flight possibilities. If it takes 4 hours to get from PVG to Nanjing, that still would be faster than connecting through PEK. How bad is PVG? Could you reasonably make it from the airport to Nanjing in 4 hours? (I'm guessing from SHA that would be no problem since the train station is so close, though is it easy to navigate?)

Are there any other Chinese destinations that have reasonable rail connections to Nanjing?