I would say that you're right, just because a place is local it doesn't mean that you should automatically buy from them over a corporate chain. Just like anything though, you get what you pay for in this hobby. For the most part I buy fish from a certain place local to me. Not specifically because they are local, but because of the quality and service I have received from them over the years. Here are a couple points as to why I only buy from him:
1) He gives me a lot of detail on his suppliers. Whenever I ask for a specific fish he'll tell me where he can get it from and what his experience with that specific supplier is with the specific fish I'm looking for it. For instance, I recently went to buy a pair of wantanabei angels. He suggested that I have him order from a supplier in MN that QT's their fish for 8 weeks prior to making them available and guaranteed the capture methods were appropriate for the fish. This was important to me because this specific fish commonly has decompression issues due to the depths it's collected at so knowing it was captured "the right way" AND had an additional 8 weeks of observation made it really appealing. The owner said he could also get the same fish from another supplier, that they would be cheaper, but would only be about a week or two removed from the ocean. Getting that kind of insight on the fish is really appealing to me.
2) The support I get from the owner is well worth the extra I pay. I have been able to call the owner's cell at midnight for an emergency and he even took in my corals when I lost power for 5 days.
This is getting to be a long post... sorry
The long short is, don't buy local just because it's local. But if there is a local store that offers excellent insight and support then keep that in mind when making a purchase. In my experience it's been well worth it.