PEK or PVG, may I suggest both, that is like coming to the US and deciding on visiting Washington DC or NYC, they are two totally different experiences.
Beijing is unique and a must visit for cultural / history and as the capital. Can be done in three days or less with visits to Forbidden Palace, Ming's Tomb, Summer Palace and of course the Great Wall. Unless you are incredible lucky expect horrible traffic and even more horrible air quality. But if you capture a good day, could be a lifetime moment. I travel every other week to China and have no interest in visiting the capital, mostly the air and traffic.
Shanghai is an amazing modern city with great transportation. Traffic is bad, not as bad is Beijing, ditto with air. YOu can see the sites in a little more than a day and half IMHO. The Bund, Financial Center, Classic old river town, and perhaps East Najing Road . World class city with world class dining, drinks and clubs, if you know who to go with
My second home away from home at the moment.
And if you are into the counterfeit stuff stop on Line 2 Shanghai Science and Technology Stop, exit two Xinyang Market and refuse to pay more than 30% of the original asking price
As to airline, UA to SFO and direct flight to either PEK or PVG. At least to PVG UA has three flights a day and can't be beat for schedule. If it wasn't for that flexibility I'm almost certain I'd have moved to AC or HU as my longhaul. Sadly my company only picks up economy
As to inter China, I'd say they are all similar people herders.
As another suggest the high speed rail is something you must try, they are decades ahead in infrastructure than the US.
Enjoy China!