I'm surprised it did not come back with an operational iPad within the hour, however that many photos and videos could take a day or more to finish transfering,
At this point I'm guessing it either started working, or you are back to square one.
If the second, you might want to choose a different method of setting up the new iPad. Instead of letting the two iPads work together, make sure you have a good backup of the iPad3, then choose to restore from that backup when setting up the iPad9.
That said, it's a really big gap in iPad models and operating systems. I don't know how it will go. If you have an Apple Store nearby, you might try setting up an appointment and having them take a look. This kind of service is usually free. They'll certainly tell you before doing anything that cost money.