You would probably be happy with either one of those bikes. The Trek's geometry is going to have you a little more upright. It has a longer travel fork and a better rear shock (a good reason to choose it over the Fisher). The Fisher has a bigger brake disc in front, but that's not as important as travel. Most of the other components are in the same range, they are from the same manufacturer after all. I think the Trek brand gets more attention from the company than GF. As an example the Fuel had a remodel in 2007 AND 2008 when they changed the rear suspension linkage. IMO the Fuel has a better suspension design. I know a LOT of people who have bought the Fuel in the last 2 years and they are very happy. Not too many buying GF.
I am riding a 15" Fuel. It is a little big for me, but the carbon did not come in a smaller frame. I adjusted to it fine. MTB's can be tuned to fit you more so than a road bike. Every bike I have bought was sight-unseen. That includes a Giant Trance 14" and my Trek 2.3 road bike. I haven't had a problem.
Dealers have to pay for the bikes in their shops. Small shops are not going to carry higher end bikes they may not sell. Makes it hard as a shopper, I agree! But small shops are great to deal with. I think it is a good idea to shop for the right LBS. Are they friendly? Competent? Do they offer free lifetime adjustments? I think these things are very important because when you buy a bike you are buying into a relationship. Hope that helps.