http://dom.retrobox.eu/?/20130910/log.516ce75de4b082c74d7a61e2.1378804318722.txt
I just barely won this one by tie-break; a few mistakes for me, the last Silver should be a Great Hall, and probably a Duchy instead of the Harem. But... what? I am playing against Apothecary/Great Hall, is that really almost as good as Wharf/BM? It seems like 6 Great Halls should only make Apothecary stall even worse. My opponent is a top-25 player. What is going on?
You're right that Wharf/BM should beat the apothecary deck here pretty easily.
Putting the Wharf down as card #11 on your first shuffle doesn't help, but the real problem is that you failed to adapt to what your opponent was doing.
Apothecary decks without draw, without trashing have a huge problem buying green cards. They will just plain collapse on anything beyond the 4th province.
You should focus your game plan on this: just don't lose on a 4-4 province split by having less Great halls. As soon as the duchy dancing starts, you're good.
The key card to this plan is Harem. You can buy them, buy lots of them, and buy them early. Your opponent can't.