All of the second episode should have been a flashback.
Think about it.
They wanted everyone in a Starfleet uniform at the end of "Caretaker". Fine. Janeway says that she and Chuckles talked it over, and agreed to that. A fitting ending to the pilot, with the course set for the series' future.
Still, while said conversation wouldn't have fit in that
ep, doesn't mean it wouldn't be interesting to see. Negotations and all. Tensions and stuff.
So, the whole second ep could have taken place between the destruction of the array and that speech.