Of course, my answer is "begin with DCC" -- didn't it make the top 5 selling game for something somewhere recently? Also, it kicks booty. YMW
I agree with you, but a lot of shops seem to avoid smaller game lines. A couple of years ago my advice would have been "begin with C&C" and I hardly ever see C&C stuff in game stores, either. Game stores often seem to start with the big companies (e.g. Hasbro/WotC) and fill in occasional stuff around that. One of my local stores has a big shelf full of stuff, but when you look closely it's all 3E/4E or Vampire stuff.
A run-down of the local strange, as I like to call it:
Barnes & Noble: D&D 4e only, and that they have moved from the book section to the toys & boardgames section of the store. They stock only the core books, minis, and dungeon tiles.
All About Games: They have two locations, one of which I refuse to visit because I hate going down town (one way streets and hipsters a plenty) - they stock a tiny bit of 4e, a tiny bit of Pathfinder, an even tinier bit of other books, have a wide shelf of reasonably priced used materials and mostly stock boardgames and miniatures for wargames.
Phoenixfire Games & Comics: Their RPG stock includes D&D 4e, Pathfinder (even some 3pp), and a smattering of Shadowrun, Savage Worlds, and Warhammer based rpgs, oh and not to forget Legend of the 5 Rings and Doctor Who. They also have a couple of DCC products on the shelf because of the extras coming in here and there when they fill my standing orders.
Then, there is Hobbytown USA: they stock everything mentioned above, and in greater quantities, as well as having GURPS, and a wider variety of smaller titles like Judge Dredd, d20 spinoffs, stuff that is no longer supported but is still in stock at distributors here and there (like the Midnight setting for D&D) and the widest variety of gaming accessories of all (dice, dice bags, tracking charts, flip mats, every kind of mini in production, battle mats, burst templates, all the cards that Paizo makes, and of course all the materials to build your own terrain).
The store the least focused on RPGs happens to have the widest variety and thickest stock - probably the benefit of being a pretty big chain, and a pretty big physical location to boot... if it weren't so far away in comparison (Phoenix fire is a literal 30-40 second drive (or a few minutes walk), Hobbytown is 16 minutes away in perfect traffic) I'd probably be there every day for a month straight just to finish really looking at what all they have there that I am interested in.
It seems backwards to me.