So form what I can tell they are puppets of the Thalmor, you often see the Thalmor advisors to the legion. If you are fighting for the legion are you really fighting for the Thalmor?
Heres my take... Although the Legion may be puppets they should not be abandoned. If you choose to side with the Stormcloaks then you will weaken the empire thus allowing the Thalmor to take the empire including Skyrim form the Stormcloaks at a later date. So you should help the Legion which will allow them to regroup and rebuild and it will also send a message to other provinces not to rebel. So in the long run the empire will be united and after a while of recruitment they will be ready to face the Thalmor once again.
I am of course trying to convince myself here... open to discussion...