I've tried ebay, amazon, and Shopify. I now only sell on Shopify. In my business (fly fishing), there is too much low price point stuff from overseas for me to effectively compete on ebay. Amazon just wasn't user friendly for me. Shopify allows me to build my own brand over time. And it takes time. No matter what your platform, if your product isn't good and you don't have a brand people can differentiate, respect, and trust, you will fail. Shopify has been great for us.
You have to assign SKUs to your products. Develop your own system, whatever works for you. I chose to use five-letter groups that consist of the initials of the maker, the product, the color, the size.
If you don't have a UPC code, you have to become a member of GS1, which means shelling out a membership fee and then paying dues. It was $900 when I joined. That lets you create your own UPC codes.
You don't just make money with Shopify. It's a branded storefront. You need to drive traffic to your storefront to make money, something Shopify isn't meant to do.
ebay & Amazon are marketplaces with milions of users and you HOPE they find you in the clutter of other sellers. You pay a premium for that user reach.
Marketplaces should be leveraged as a new customer acquisition tool. You then market to those new customers to come to your storefront for any future purchases.
Best option is to do both. You'll make more in the long run through your own storefront but driving traffic is the hardest part.
We have had a good deal of success selling on Shopify. However, I would caution that this moderate success has started to come in now that the site has had some decent SEO and authority building over the last six to seven months or so. We are embarking on some pay-per-click advertising now - just dipping our toes in the water, so to speak. Our strategy is to maintain the SEO and authroity building, and to start using some of the advanced targeting available through PPC to enhance our position, especially now that we have some metric to see WHERE we should be advertising.
Perhaps we'll look at Amazon and possibly eBay down the road, but it is our firm belief that a platform like Shopify was the best foundation for us to build on.