With all honesty, I think the world needs more stores like Aquarius Records. You could model something after them: A place where you only have a handful of people working, each specializing in different genres: e.g. metal, punk, indie, prog, etc. (Let's face it, just selling metal alone is going to be near impossible.) And a website that sells CDs at competitive prices like Erik said, but with a paragraph write up for EVERY catalog entry and an MP3 sample.
Also go digging out new bands from all four corners of the globe through trading etc and come up with some real wacky stuff like rare 7" Eps and wotnot. In the meantime, run a cool label on the side where your store can act as distributor.
Shit, if Aquarius wasn't so expensive (yes, anything $13 and more that doesn't include shipping is damn expensive in the US), I'd buy from them every other week.
I also agree about location. I mean, Aquarius works because it's in San Francisco. You need to find somewhere equally bohemian, like Greenwich Village, NY or Cambridge, MA. Although all those people are either tourists or poor students....yeah, San Francisco is the place to be.
All roads lead to Northern CA!!!