We registered for a lot of our more expensive and hard to find items on amazon, since the prices are lower than stores and they have some rare stuff.
Then, we registered at Buy Buy Baby for the majority of our necessities (clothes, safety supplies, etc.) Both our families really like to buy there in store, so we figured this would allow them to have some fun shopping.
We also registered for some supplies and items at Target, mostly daily things like Burts Bees lotions and bottles. This is where a lot of our friends shop.
Even though we didn't plan to, we have two items on a registry at BRU. The breast pump I want and the bath tub we like aren't available anywhere else. We're only sharing this registry with my mom, since she planned to buy us those items anyway.
We considered cost and our shower guests when building our registries. Most of our family and friends will want to buy in store, so BBB and Target will give them some options (there is only one BBB near us and out of state friends/family can still visit Target - which was where we registered for our wedding.) The amazon site is great for friends and family who are a little more tech savvy (86 year old g-ma is not going to be ordering online!) or plan to purchase the more expensive stuff (my MIL can save $150 on the stroller and carseat she would like to buy for us!).
I don't see a problem with giving people more options, but keeping track of the items to ensure the lists don't overlap could be tough. The way we see it, if people choose to purchase from our registry (since registries are just suggested wishlists, and not everyone will use them) we already did the price comparisons and browsing for them. lol