1) The Note3 has so much internal storage that you have to be a real software junkie to run out of internal space. I've been looking for stuff to download to mine, just to see how much junk I can put on it, and still have loads of internal space left.
2) The Note3 is fast. USB 3 (vs 2) doesn't change that for playing apps that are in the phone. It will speed up transferring files to and from your computer.
3) A Class10 card is as fast as they get right now, but with 16GB internal, it's going to be some time before you need the extra space. I wouldn't start worrying about that yet.
I just checked my storage. Out of 32GB total, I still have 22.96GB available, and that's with all sports of junk I tried, didn't like and haven't deleted yet. I don't store movies on my phone, but an .avi movie can be less than 1GB, so even with a few movies there's still plenty of internal space.
As far as speed, unless you're doing intense scientific calculations, even a Class6 SD card is fast enough to play a movie. You've got a Cadillac and you're worrying about whether the sticker on the license plate is going to make the ride bumpy. Relax and enjoy your Note3.