As I understand it if you resign from your squadron you have to start from the beginning with the new one and there is no way around this.
PS: I am also told that the easiest of the Imperial Squadrons is Black Epsilon.
EDIT***
Here is a cut and paste of the process from the official pilot boats at SOE...
Changing Pilot Factions:
To switch squadrons or if, for some reason, you need to restart your current squadron, follow these steps:
1. Make sure you have at least one open slot for your new starter ship.
2. Go see the Pilot recruiter for your faction. Not your trainer, but the recruiter. For instance, if you're a Freelance Pilot, you'll need to see Gil Burton in the Bestine hotel on Tatooine.
3. "Resign" from your current Pilots' faction.
4. Go see a faction recruiter (if needed) to quit your ground-based faction. [You must be a combatant and not "on leave" to resign from a ground faction.]
5. You will need to start over with your new Pilot squadron from scratch. Your space xp will be set to zero when you resign your Pilot skills.
NOTE: For each Pilot faction (Alliance, Imperial, Freelance) that you master a squadron in, you will receive the "Previous Faction Master Bonus". The maximum bonus is 3x, if you master at least one squadron from each faction. This bonus adds to the normal Space Combat Experience you earn, for a total xp of 1x/kill for 0 faction masteries, 2x/kill for 1 faction mastery, 3x/kill for 2 faction masteries, and 4x/kill for 3 faction masteries. You don't get a bonus for each squad mastered, but for completing any of the three squads in a given faction.
Edited, Dec 23rd 2008 8:41pm by MontyB