Drupal Commerce is also an open source system and is very, very customizable. However, Drupal Commerence is much more complex to design compared to Ubercart. A little programming experience is needed to successfully set up an online store that functions smoothly.
Now let us see the differences between these two softwares
1. Product management. Ubercart is easier to use in product management because it treats each product as a same node, and the different attributes of the product as color of pant, or size of hats, it treats them as attributes of the nodes. On the other hand, Drupal Commerce has different nodes for each combination of the products. For example: if you want to sell dresses with the sizes L and M, and with the colors blue, red and green you will have to create six nodes. The advantage of this is that you won’t have errors with the shipment and tracking, because you have the variation of the product as one node, were as in Ubercart you have one node for all the variations so it is likely to generate some errors with the order.
2. Shipping and payments. Drupal Commerce does not come with a payment and shipment module; you will have to install additional modules. As of Ubercart, it comes with the two modules and you can choose from a lot of payment methods, and with Drupal Commerce you cannot implement payments with Google Wallet and no shipment with FedEx. This is the same with other modules because Ubercart keeps its functionality inside the core, however in Drupal Commerce you will need to install additional modules. The idea behind this in Drupal Commerce is to divide and conquer concept, i.e. it allows the user to install only the modules that he will use in his e-commerce shop.
3. Learning Curve: Drupal Commerce is more complex to learn, were as Ubercart is much easier to learn and it is more similar to other e-commercial software.
4. Configuration: in both of them is fine to leave it with the default configuration. In Ubercart you need to change address, currency and contact, were as in Drupal Commerce you need to check settings for payment method, pricing rules and currency.
5. Documentation: It is far better of Drupal Commerce than that of Ubercart.
6. Long term: In long term projects it is better to use Drupal Commerce because you can expect more enchantments in the future, were as Ubercart restricts you from designing large stores and might be outdated in future.