It does make it very difficult to place the characters and/or the U.S.S. Enterprise in jeopardy in the story when a character who is omnipotent is included in the story.
Q has lost his powers, and restrained or refused from using his powers. He also has "superiors."
And what if there's something out there stronger than he? What if the continuum faced a threat?
If I was in a meeting where a Q movie was being discussed, I'd start at what Q said to Picard at the end of AGT - that his future lay not in cataloging planets and what not, but in exploring the "limitless possibilities of existence," and then he went to tell him something, but stopped... what was he going to tell Picard, but didn't?