The big problem with state-level marijuana-legalization is that the state can make it legal, but the federal DEA still aggressively prosecutes marijuana distributors.
(I live in CA, and I have 3 MJ dispensaries in a 10-minute walk from my house; 7 more if I want to drive five minutes.)
You have raised an important point. This has turned out to be a problem in CA.
Pharmacies don't want to touch MJ because it's illegal under federal law. The regulatory arm of the state of California doesn't want to touch it for the same reason. Some cities attempt to regulate it, some don't.
Because the dispensaries produce a lot of cash profit (in violation of prop 215, but whatever), they have been able to fund lawyers to sue cities and invalidate all regulations. It turns out it's really hard to craft a regulation, even a simple one for licensing, that holds up to court challenge. The city of LA has given up and explicitly called in the Feds to raid the MJ shops. (The feds get them for tax evasion -- kind of a catch 22 because it's hard to report this income on your federal return; as mentioned, they're not supposed to profit but there's no way to check.)
I voted for Prop 215, but I really had no idea how quickly it was going to turn to shit. Pothead idealism meets serious potential for quick profit.
There's an interesting parallel to marriage equality. Full marriage rights are still out-of-reach while we still have DOMA preventing things like survivorship benefits at the federal rights.
http://www.westseattleherald.com/2012/08/27/news/dea-orders-...
Full legalization can only be done at the national level.