Last time I went to the Pomona store, I saw a few items that weren't at the Fullerton store. Nothting major but it was noticeable. (they had more toys and pins and a few collectible items)
I hit up the fullerton store last week and an employee did confirm that most stores will carry the same stock, but the various stores do indeed get a few extra things that won't be at the fullerton store and vice versa.
Either way, wherever you go, you're gonna get cheap Disney stuff. For anyone closer to Pomona, it's not a waste of time. Plus there's a Mattel Toy outlet right next door. (definitely not a waste of time for holiday shopping).