As I already said in this thread:
http://forums.civfanatics.com/showthread.php?p=12621794#post12621794
I think a lot of criticism concerning the Commerce tree comes from people misunderstanding its purpose (to which, imo, the name somewhat contributes). Commerce is not, imo, for civilizations that focus on trade (there is only one policy that gives a direct bonus to trade routes) and (unlike G&K) it is not for civilizations that want to win a diplomatic victory. Commerce is for civilizations that want to be self-sufficient in terms of gold and happiness, without running into deficits and rebellions - i.e. warmongers. If you want to run a peaceful trading tall empire, Commerce is not for you, imo.
But when you have a wide warmongering empire, with a lot of puppets and everybody hating you, then having more great merchants to settle and getting bonuses from trading posts is what allows you to keep a positive cash flow - and being able to buy cheaper buildings and paying less for roads connecting your wide empire is also a huge boon.
As for the weakest tree, I think it's Exploration - mainly because the finisher is so lacklustre compared to other finishers and it focuses heavily on navies and Great Admirals, which is very situational. No matter what victory you are going for, I think there are better alternatives to Exploration, and you only want to open it to unlock Louvre if you are going for a cultural victory.