I launched a small e-commerce site that integrates Hybrid Core and WooCommerce. I was responsible for design and development. I'm not much of a designer, much less for feminine sites, so don't judge me too much : )
The development was interesting. You can read why I used Woo instead of Jigoshop (the e-commerce plugin it was forked from) in another thread, but I'll speak of the development of a WooCommerce theme, as it's most applicable, though they're both very similar.
There are hooks everywhere in WooCommerce. You can filter and add functions to your hearts content. The code was well organized and fairly easy to find. There's a templates folder, but more importantly there's an actions and functions folder. This makes WooCommerce quite customizable, and easy to enable / disable / change things from a single theme setup function.
You can also completely override templates in a custom 'woocommerce' folder in your theme directory. You can override quite a few templates this way. Just be careful you don't override a hook that has an important function connected to it and not program it back into your template.
The only other issues were deregistering and registering the shop wrappers to work with my theme, which is well documented how to do. Finally, I really don't understand why the plugins even have a call to get a sidebar. They shouldn't do that at all in my opinion, so I took it out.
CSS can be done a few ways. You can override styles in your theme directory, but you may get stuck having to use !important a few times that way. It's best if you're doing a parent theme to just not use WooCommerce CSS, copy their css file, and include it in your theme to edit that way.
Variable products in WooCommerce are awesome. Granted, this site has waaay to many variations per product, but the way it handles them is much better than Shopp (the other e-commerce plugin I have familiarity with variations). Most of what I mean by this is the ability to use *any* x *any* variations so that if you have 3 colors and 5 sizes you don't have to configure 15 variations.
I'm sure this site still has bugs, and the owner wants to spice some areas up a bit, but all in all it was pretty smooth. I hope this may help some of you.