My experience with Instacart for Whole Foods delivery has been pretty bad overall. Too many items were consistently being marked as not available / not found by the shopper. Once, up to a third of my cart or almost 10 items. When you assembly your list and click "buy", you expect to get what you ordered, not for a third of your order to be missing come dinner time. I'm afraid Instacart won't ever be able to deliver a great experience as long as they have shoppers walking the aisles instead of direct back-of-store integrations and real time inventory.
The substitutions offered are also frequently terrible, and always without fail for more expensive items. Sometimes ridiculously so. And I'm pretty sure the shopper sometimes just doesn't want to buy some of the stuff I've ordered, like watermelons or water, that I know is available in the store.
Overall, I've found FreshDirect to offer a much more reliable service with good pricing and selection as well. They seem more professional in all regards. I also look forward to seeing what Amazon / Whole Foods come up with together, but I don't think the Instacart shopper model is something I'm interested in using again, it just seems like a fundamentally inefficient model.