I completely agree. I think Vaughn being with Syd is a part of that - but I guess there isn't much of a storyline to play on with Will. I'm sure he'll start having a bigger role because of this whole Francie hypnotizing him thing.
Also, when Will was the only person who she was close to who knew about the CIA/SD6 thing she talked to him a lot more. Now, she can talk to Vaughn.