There is no deciding. Read the dev blog. At the end it list all the Alpha skills. If you are not an omega, those are the skills that you have access to and can train.
So for example, I have advance weaponry to 5. If I unsub and am an alpha, though I still have the skill to 5 the game treata it as capped at level 3. If I go omega again, it will be treated as 5 again.
So there is no deciding.