A couple of months ago someone made the recommendation to shop for a bike shop first, then a bike. Since the fall I've visited at least 10 shops covering a wide spectrum, from a place selling predominantly fishing gear and bikes I would expect to find in a garage sale to the high tech Cannondale store in Natick Massachusetts. Here are a few observations in helping you discern a good shop from a mediocre one. I hope others will also add to the discussion.
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\n1) Repair areas: coming from a manufacturing background, I'm impressed when the work area is clean and organized (5S for those with similar backgrounds). It makes repairs quicker because the mechanic isn't hunting for tools, using the wrong tool (like using a screwdriver as a chisel) or tools whose damage is covered by grime. It all tells me the care about there work area, the work they do and ultimately my bike.
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\n2) Bike fitting: my Giant escape came with a free 5 minute fit. Awesome, the seat height was adjusted and off I went. Most do something between that an hour fit. The Cannondale store does a comprehensive fit utilizing their Guru system. My best experience was with Bicycles East in Glastonbury, CT. They did a 30 minute fit just to determine what bike dimensions and size were right for me. They then made a recommendation of what model and size would work best for me (Because of my longer legs and shorter torso a Trek Domane in a 60 with a modified stem). This was by far my best experience. I truly felt like they were trying to find the right bike for me as opposed to the best bike they had in inventory. If I purchase the bike they'll then follow it up with an hour of fine tuning. They also have more extensive fitting for a price.
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\n3) Tune Ups: most offer one. One place offered free tune ups for 15 months. They also offered appointments. Very convenient.
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\n4) Warranty: most have the standard lifetime frame, 1 year components. I came across one place who extended the components to 10 years. They also made it clear that they'll work any warranty issues with manufactures, even swapping parts from a new bike so I wouldn't have to wait.
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\nHope that helps for anyone trying to discern an average shop from a good one. Looking forward to hearing other recommendations and experiences.