i'm in pretty much the same position. just got a new bike (up in washington, and i live in california) - i'm going to the LBS that seems the friendliest and most helpful - there's a few in my town - but like yours they had hardly any selection and none in my size or even for my gender (F)! that's why i ended up getting my bike in washington (AND i got a smoking deal!)
i'm new to (road) cycling as well so i'm just trying to take it all in right now! i think establishing a good repoire with a solid LBS is key for someone like me, just getting into it. so anyway, i know that doesn't answer your question - but i think you should just go with the shop that you liked the best, even if they don't have great selection right now.
good luck!