On thinking about it, I'm not really a huge fan of a free FCS on the advanced. It is very out of character for the rest of the ships and modifications in the game. I'd actually suggest something like this:
Advanced Targeting Computer: Tie Advanced Only (or, potentially Imperial Small based only)
Modification, 1 point
When this ship takes a TARGET LOCK action, it also gains a FOCUS token.
This modification would be similar, yet more powerful than the FCS, though it would cost a point. In general, it would provide the non named Tie Advanced with a limited version of Push the Limits. It doesn't really break Vader any more than he already is, as vader would have to choose between Advanced Targeting Computer and Engine Upgrade. The biggest benefit, in my eyes, is that it would follow the standards set by other upgrade cards and ships a lot more than giving the Advanced an existing card for free.