I’d argue that, at this point in time, working with WordPress taxonomies has never been easier.
Sure, creating, tagging or categorized, and adding custom taxonomies to posts and custom post types has always been relatively easy, but when it comes to implementing a solution that utilizes custom post types and/or custom taxonomies, then constructing queries can sometimes be a bit of a pain.
But now, we have more API functions and features than ever before:
Of course, there are still cases in which retrieving and organizing data still leaves something to be desired.
I don’t fault WordPress for this, though. It’s more of a function of how data is ordered within databases, applications, and in computers in general.