-We planned our 6 week Asia and all the Disney parks trip completely on our own
-If you have to choose 2, make sure Tokyo is on that list.
-I would consider time to be a deciding factor as well, you could easily do HKDL in one day, but SDL takes at LEAST 2 days.
-Hong Kong is small, but wonderful, VERY similar to DLR, and has some INCREDIBLE shows, and top notch rides that aren't anywhere else (Mystic Manor & Grizzly Gulch)
-Shanghai is HUGE, beautiful, new, with lots of stuff to do, it's definitely worth seeing.
-Tokyo should need about 4 days, but again, depends on your plans. It's my favorite Disney park from all around the world, hands down!
Transportation for Tokyo & Shanghai is SUPER easy, we were at AirBnB's for both of them and it worked perfectly. Tokyo has busses running from Kasai station, and trains running from all over. Shanghai has a train line that goes right to Disney as well, it took us less time from our Bnb to the park gate than it would to get to MK from All Stars, lol!!
HKDL however, you CAN get there on the metro but it's a bit trickier/takes longer, because of that we chose to stay on site, and really enjoyed it. The park does open later than expected though so you'd have more time from the city to Disney.
Were you planning on doing things outside of Disney as well?