I'm sure it will have a good enough flow, since they're making new and remaking old ones. Plus, Nomura's directed a film before. He has to know what he's doing.
If it flows like a movie, I certainly hope that it's better than Advent Children. :/
^then prepare your imagination.....
For possible missing boss fights.
That's not much of a problem. Creating a good fight scene would probably waste good time anyways. Most the Disney stuff isn't even related to the main plot anyways.