Curious, what inspired the itinerary to begin with?
I do PEK-SHA at least once a month, often more. Without a doubt transiting Hong Kong (or anywhere else) is the
worst way to do this itinerary
, from a strictly time and convenience perspective. I couldn't recommend that itinerary to anyone.
As for best way, I may ruffle some feathers here but I don't say it's as clearcut to take the train vs fly. Flying is still better on most days. The problem is the bad days, of course. But the high speed train departs from Beijing South, which is a longer drive to reach than the airport from many parts of Beijing (especially central, north, northeast and east). That's because PEK is situated northeast of the city, while Beijing South is...south. I got to enjoy an hour 30 minute drive from Haidian to Beijing South two weeks ago and cursed not taking the plane, which naturally was running without delay given my luck.
Then, most flights still operate from PEK to Hongqiao (SHA), which is next to Shanghai Hongqiao HSR station and hence the same distance from wherever you're going in Shanghai. Much better than Pudong. The fastest trains are still 4:20, and because of Beijing South's "not so great" location, you don't end up saving a huge amount of time on the front end. Even if the flight is an hour delayed or more, you still come out ahead flying. It starts to become a wash around the 1:30 / 2 hour delay mark.
What HSR lacks in speed it definitely makes up for in lack of insane delays. Flying is superior 3 or 4 out of 5 times. But when it's delayed, it can be awful and then you curse yourself for not having taken the train. Case in point, my flight in March, which was 8 hours delayed SHA-PEK...
But another problem with the trains are frequencies of the fastest train sets were cut back, when the speed was increased for the "Rejuvenation" (FuXing) train, which cut off about 30 minutes from the old time. But because of this upgrade, the fastest trains aren't even going every hour anymore, and 1st / biz seats sell out fast, sometimes weeks in advance for the popular times. (2nd class is usually open). Meanwhile, there are tons of trains running PEK to Shanghai but they're 5hr30mins - 6hr30mins, which makes the train a really unattractive option in my opinion. For me, the GX or GXX trains are the only realistic options (which are between 4:20 and 4:40), and I'd probably only do it alone in biz class or with a colleague in biz or first. (in Chinese high speed train world, Business Class > First Class > Second Class). Business Class is a nice flat bed.
I'd still look at nonstop flights and cross my fingers. That's my two cents. I take that train probably once every 6 weeks, and fly maybe once every 3. The train becomes more of a no-brainer at under the 3:45 mark. Or, if there were more of the fast frequencies, which there presently aren't enough of. Not quite there yet.