When 2 level bases are implemented, what about different base layouts being made available for the initial base? Since the initial base is configurable, there could be multiple different base layouts offered to the player, eg
1) Current base (or a 2 level version)
2) Extra labs (20 or maybe 30 lab space)
3) Extra workshops
4) Extra hangars (2 interceptor and 2 dropship hangars)
5) Extra defences
6) Base : Sparta (just the required buildings and a radar, no hangars, no or little living quarters, no hospital)
and so on. Maybe some have labs or workshops, but not both, or extra defenses and extra labs, but you get less starting cash.
You could even tie in the difficulty system, where lower level games not only start with more resources, but can choose any base type freely (100% chance for all types), but as you increase difficulty, you get a more restricted choice, and maybe even just have to take what you are given (which might still be exactly the base you would have chosen, or maybe certain base types are forbidden at higher difficulties)