San Diego has such a varying assortment of shops.

I base all my opinions on shops off of the shop I used to work at. Selection, size of the store don't really matter to me. What it comes down to for me is, the staff and overall feel of the store. I'm not a huge fan of the uber coperate (IMO) stores, ie BL in Pt. Loma (Nothing but specialized) and the Trek Stores.

I am however a huge fan of B&L in Solana Beach and Nytro. Both shops have been great experiences for me. Plus B&L is a Twin Six dealer that usually has an awesome selection of their Jerseys.