Sure, WPEC works, and well from what I can see, but dealing with it is irksome. It lacks a certain intuitiveness and to me the fact that you have to pay $47 bucks for the presentation options in Gold Cart, though they throw in some payment gateways as well, just seems weak.
On the topic of Payment options, WPEC does not offer a PCI compliant Payment Gateway, unless you count PayPal Standard. Their Mijireh plugin costs $69 bucks for what is a "Free" Service (Mijireh takes a cut of your sale as payment). WooCommerce packages both PayPal Standard AND Mijireh in it's plugin.
There are just to many little annoyances in WPEC that seem to not be an issue with WooCommerce, not to say WooCommerce is perfect. However, it does seem that WPEC users are very much left to their own devices for things that would not be an issue in a more polished plugin.
It seems that if you're a coder, WPEC may be for you. If you like getting down with PHP, CSS, and whatever else go for it. I'm sure you will find a way to work out the kinks. If you want something that works and is more polished, look elsewhere.