I don't think much of Kragen either, though they have gotten a little better since they were sold. A good auto parts store will give you good advice, do things like test alternators, starters and batteries, perhaps do basic machine work (rotors, drums and flywheels) for you, and so on. Kragen will pick random words out of a Haynes book.
A really good sign is a set of parts guys who do their own repair work on their own vehicles. It's hard to find this in a national chain. Sometimes an individual store from a national chain can be good; it's a crapshoot.
But factory "original" brake pads? Since when does Honda make their own pads? They come from a third party. You can probably find the exact same pads elsewhere. Look for the stores that supply nearby mechanics.
It's possible that your "Honda guy" really believes he's getting better stuff from the dealer. I've seen stranger. But, more than likely, he's getting his own shop's stuff from an auto parts store as well, because the pricing makes him more competitive.
Virtually all mechanics do "services." They are usually not necessary, unless you never read your maintenance schedule. If you frequently work on your own car (including pre-roadtrip inspections), you'll take care of most of it. These services are a way of selling more work, as you can look at a mildly overtightened radiator hose and say it needs to be replaced (really, you can wait until it shows signs of seeping coolant -- but not any longer than that), and make $100 on the simultaneous flush'n'full and the thermostat and rad cap you "might as well" replace along with it. Oh, and your water pump has 50,000 miles, you might want to do that, too (IRL, not unless you see evidence of corrosion around the weep hole).
