Nothing this season has made sense anyway. The idea of doubling people is insane anyway- who would've thought we'd ever see that on Alias (so cliche) & it was done. Doubling people for virtually meaningless tasks (like what they did with Lennox & Francie in season 2) doesn't make sense either but it was done...if you had that technology, you could do some SERIOUS damage not just hypnotize poor Will Tippin into giving you satelitte info and eavesdrop beginner's style on Sydney & Vaughn
I don't even really get why they needed to brainwash Sydney only to send her off in the somewhat dangerous pursuit of the cube? If she was so important, why send her to do something any skilled agent could do? It's just seems so risky...
I agree that the Sydney we know is definitely not a double. All I'm saying is that it's possible they doubled her to use at a later date as an asset...not to take the place of the original Sydney like they did with Francie's double. Just because you have a double doesn't mean the original is useless or without her original value to them- it just means they may have advantage of some kind having someone be able to pass herself off as their precious Sydney. Remember the real Lennox was alive...it doesn't seem to matter because doubling is so otherworldly, you can't really think about it rationally. Anyway, it's like this season wasn't even thought out at all...it's like they're writing whatever happens to fit at the moment they sit down to write