Shopify DOES NOT help you sell. Period.
Amazon will win in the long run because at the end of the day it's all about if the "platform" can move merchandize or not. Amazon captures top of the funnel all the way down to personalized targeting.
Shopify will never do that. they are just the tool to help you figure out all that yourself. Outsiders / beginners looking in would say Shopify is amazing because the ecosystem and how many "tools" there are to help you sell. but it's all load of horsesh*t. The merchant ultimately is the one responsible to run the ad campaigns, find the customers, run promotional pricing on BFCM.
There's a lot of misconception of how much hard work it is amongst beginner Shopify merchants in order to generate sufficient traffic. Amazon, at the very least, provides an audience -- which solves a very major problem for any business (to get traffic).
There's a lot of success stories running on Shopify, but these companies would have pretty done well creating their own custom solution.
At the end of the day, it's a piece of software (ie. shovel) to sell to people who want to try and make money online (ie. the gold rush).
I agree that most small companies aren't up to the challenge of managing an online business. The 3PL integration will help a little bit, and I imagine that Shopify will continue to chip away at the problem by integrating other services.
Seems like if Shopify is a way to create your own venue, and Amazon is a venue in-and-of itself, there might be a case for doing both.