I think the problem here is that it was after two dates, and it sounded like it was basically a short email to say "I enjoyed my time with you." If he'd said, "I really like your hair, your smile, the way you talk, your intelligence, how creative you seem to be, and our conversation," it just gets to be a bit much and might come across as creepy. Honestly I don't think people should be talking about smell quite so soon in a relationship, though. I think that remarking on somebody's smell is a bit intimate and should be something reserved for later, once a solid relationship is established.
This is true as well. An ex-friend from college was one of those types that come on way too strong and tend to jump into the emotional intimacy way too soon. In hindsight I'd say it was a lot of red flags. So if someone did start praising all those qualities I'd be warning a gal to be cautious as ot would sound insincere or trying to hard to appear like Mr. Right.
So yeah best thing he could have said? "You looked great, enjoyed our conversation." Bit in all truth, if she didn't like him she'd dismiss him no matter what he did.