Some bike shops seem to be populated by snobs. From what I read in bike forums, some wont even fix a flat on a recumbent or a trike.
As far as upgrading "walmart" bikes, why not. Some that I have seen have some really trick suspensions. Derailers that cant be serviced should probably be the first to go, followed by the brakes. Of course the bike will be heavy, but probably quite reliable. Riding a $5000 bike to work, and having to park it outside doesnt make much sense either.