We're running a project with Drupal Commerce and it a great base for a store, but I'd say the key decision whether to use it is how comfortable you are with development. Commerce is a well designed e-commerce framework done the "drupal way", but unless you're comfortable with writing some custom modules to fill the in the gaps it's a lot slower getting up and running then UC. If UC has what you need out of the box it's likely the way to go from a time-cost of development point of view. If you're looking for long term longevity and future upgradeable of the project and you're ready to do some custom work then consider commerce.
For our project the store we're making is very customized (you order prints online) so commerce is an excellent framework to build on. But if you need something more simple like a say a clothing store, the current way you make a product in commerce is cumbersome. To create a basic product you need to create all the commerce "products" (EG product variations or SKUs) one at a time, in a commerce product type, and then you relate them to a "product view node". When a shopper sees a single product they see the product node view, which bundles up all the (commerce product) variations. There's logical reasons to do this but its slow to enter the data.
This is a lot more work - make all the variations, and then link them to the product. There's some contrib modules out there to help this but commerce is a fast moving target so you'll see commerce updates break these modules - so that's where your ability to modify / write modules becomes important in deciding what system to use. Commerce will be likely be more challenging to develop in right now - as it's got it's own learning curve, but its nice that basically everything is there is now drupal core stuff : views, fields, etc. So if you need flexible expandability in the long run commerce is great, but if your store is not likely to require future functionality enhancements and UC does what you need out of the box then I'd suggest going that direction