I do like the user interface of WooCommerce, it fits quite nice into WordPress. What I don't like about WooCommerce is that they don't care about backwards-compatibility. WordPress Core is very much into backwards-compatibility, and I think plugins and themes should follow that idea. I do wish something better then WooCommerce would show up for WordPress.

And another thing, that I personally don't have much of a stake in, a lot of WooCommerce addon plugins are of dubious quality. Following the Wordfence blog about security issues in plugins, there are often Woo plugins that have quite some big issues, like unauthenticated SQL attack or similar. As a hacker you don't even have to go to the trouble of multi-staging several security issues to get in, 1 of these is enough.