Your question is pretty broad, but I'll give the opinion of someone who runs two ecommerce stores.
I think there are two types of stores. I call them Handful (as in a hand full of items) and Boatload (of items). So if your business is only going to sell 1 to 50 different items then that is a Handful. If you store is going to sell 100 or more items, then that is a Boatload. 50 to 100 is the fuzzy zone.
There are LOTS of ecommerce systems out there for the Boatload stores. You know the style: A homepage that shows all the categories / Category pages that show the sub-categories / Sub-category pages that take you to the Product pages / Product pages with the details and the Buy buttons. These sites need to be this way because of the boatload of items they are presenting. Trying to recreate one of these is probably a waste of time because businesses that have such a big investment in their stores want a well-known established ecommerce provider (like Magento, Yahoo, etc)
But there is not much out there for the Handful stores - and I think they are the best type of stores. They focus on information rather than categorization. So they can rank better in searches. If you want to be in ecommerce and are not already a big business, then these are the place to be.
For a Handful type store you need just 3 things:
1) a website (may or may not be hosted by the shopping cart provider)
2) BUY buttons and VIEW CART buttons that you can put on any website (preferably HTML buttons, but maybe JS buttons)
3) a Shopping Cart system to allow people to gather items, learn their shipping cost, and safely pay (safely paying is most important and most difficult)
My ecommerce stores (easydigging.com and bestdryingrack.com) are Handful type stores. They rank well and provide a decent income. I use UltraCart because it provides requirements 2 and 3 without much headache or effort.
Besides UltraCart, I also know of AmeriCommerce that can provide 2 and 3. Ecwid is another system I explored that I think still fits the requirements.
I'm not sure if you want to be a ecommerce retailer, or be a creator of ecommerce systems. Either way, check out the three systems I just mentioned.
I hope this helps you. Let us know...