This reminds me of early last season when I traded Holliday straight up for Bay just before Bay had that explosive surge, but felt that this deal could level off by the end of the season...surely, it did.
I think statistically, Bay and Holliday could wind up being the same player, but the approaches at the plate are a bit different. As noted before, Bay takes his share of walks whereas Holliday had shown signs as a hacker, but the contact rate for Holliday was exceptional. Holliday projects to be a for-average hitter, with a .330 BA being on the high end, but I'd safely put him down for .300. In a debate such as this where one has the edge in valuation based on BA, puts a case of valuation in flux. I don't believe either has peaked.
I believe the case of differentiation in lineup protection is marginal. Obviously if Bay hits 5th and behind Laroche, his valuation takes a bit of a dip, but Holliday gets a slight nod in lineup protection mostly because of the promise of the likes of Helton, Tulowitzki, and Hawpe behind him.
If I had to choose one, I'd say Holliday by a nose, but wouldn't be surprised at the least bit if they both are statistically similar.