Just as a note, the faction you guys start with doesn't necessarily mean the whole game will go that way, nor is it a statement on whether your character is good or evil. The most likely beginning is Neutral (or Rebellion if everyone strongly wants to go that way), and characters' sympathies and the events that occur around them can draw them to a given side over time.
During play, your characters' actions can influence how things go, and both sides have good and evil people in them. Not every Imperial is a heartless monster (more than a few Alliance heroes started out as Imperial officers who defected over the years), and not every rebel soldier will be a paragon of virtue, and some can even switch sides and join the Empire. Even Vader wasn't above hiring alien bounty hunters, so not even race is a hard and fast rule about what possibilities are off limits. Don't worry too much about your initial choice dictating your alignment or the future of your character, just use it as a starting point.
EDIT: Almost forgot...
General plan was to have him being a veteran of the clone wars, then ditching the army once the emperor unveiled his new clones and/or the kaminoan rebellion.
Haven't decided on the service branch yet though.
No problems here; a lot of clone troopers became dissatisfied with the decision to allow non-Fett clones and non-clone recruits to join the Stormtroopers after the Clone Wars, and with no rules I could find that dictate that a clone dies earlier or the like than normal, you're basically a human that reached adulthood at a MUCH younger chronological age. Of course, if the game goes Imperial you could easily be a rebel spy, or maybe have a change of heart, or who knows what. In any case, there's no issue with being a former clone trooper.