My thoughts are that the LBS makes more of a difference than the bike "Brand" name. I own Jamis brand, because that was the best bike shop for me to deal with in the Omaha/Council Bluffs area. The quality of service means a lot to me. The bike frames might be different in geometry, but as long as you get a bike that will fit you, I could care less what it says on the frame. I have friends that own Trek, and other brands, but we don't care what each other has for a name on the frame.
Good luck with your purchase and go with what you feel is best.
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2007 Jamis Ventura Comp
2006 Jamis Explorer 2.0
2000 Specialized Hardrock (bought used)
Swim, Bike, Run and sounds like fun