When it comes to E Commerce sites, I like to craft the solution around the client's needs. Typically I focus on things like PCI Security Compliance, ease of backend maintenance for the client, social marketing integration tools, 24 hour support by the vendor, customer relationship management tools, a proper invoicing and inventory management system, credit processing and shipping options.
Focused on features that will help your store do everything you want for your business, the platforms I use support tools such as email marketing, site coupons, product reviews, blogs, product up and cross selling. I could go on and on about features for hours but as I've stated, I prefer to craft each solution based on your needs.
A solid Content Management System, for the client, is also something I consider very important. This is the system that will allow you manage your orders and store items, and possibly do simple site updates depending on the design framework being used.