I think they can't really be compared. Prestashop is a software created exclusively to create online stores, while Woocommerce (Wordpress) is a plugin that adds sales functionality to a website created with Wordpress. The differences between the two are many, let's see:
Regarding the design and themes:
WooCommerce
WooCommerce themes and design listings are really sorted. Which makes it easy to use for the new store owners using an online medium. The storefront which is another plugin in collaboration with WooCommerce has themes for free.
Themes in Woocommerce
Advantages
The themes are sorted on the basis of industry type.
Customization of themes and designs available. In case, the themes available do not suit your style, you can always customize them in WooCommerce.
Disadvantages
No disadvantages that can hamper your business.
PrestaShop
PrestaShop, too, provides different categories for themes and designs listed neatly. But, here comes the twist none of them are free.
Categories of themes in PrestaShop
T59hemes in PrestaShop
Advantages
The choice range is very vast. It has thousands of template styles in store.
Most of the themes are of decent quality. The premium ones especially are class apart.
Disadvantages
There is no customization available.
The installation of the themes is a tricky task. It sure will prove to be a nightmare for a newbie.
Regarding the price:
WooCommerce
Advantages
WooCommerce Storefront themes are Completely Free! and they have decent quality to it.
Even the non-free themes are not that costly. Most of them come for $39.
Disadvantages
The quality can be a little lacking than the premium templates of PrestaShop.
Prestashop
Advantages
The quality of Prestashop themes is a few steps in the lead. As we already pointed out that Prestashop premium templates are really classy ones.
Disadvantages
Although the categorization is done neatly, the rate of each template is way too high. The price ranges from 59 Euros to 99 Euros, whereas a larger number of theme costs 89 Euros. Which roughly converts to $68 for the least and $112 for the dearest.
No free themes are available.
Regarding customization:
WooCommerce
Advantages
Offers customization in themes, modules etc. Since WooCommerce is an open source CMS, it is re-writable by the users itself.
It offers easy customization policy. It has add-ons that can be applied as it is. In nutshell, no extensive coding skills are needed.
Disadvantages
Add-ons are plugins that are to be installed first in order to use.
Prestashop
Advantages
With PrestaShop, you get access to over 3,000 modules, which you can use to add almost any feature you can imagine to your store.
The modules can also be customized.
Disadvantages
To customize each and everything on the website, you need to be an expert in Coding. Though there are customization modules available as add-ons. But, there is a price to it which ranges from $29 to $299.
And more, and more…
I prefer Woocommerce for its versatility and ease of use and configuration, but on tastes ...