So far the biggest issue for me with WordPress is poor support for media files:
No built-in support for any categorisation of media files.
No built-in support for Retina.
Limited support for intermediate image sizes. For example I need 320px-wide images for screenshots in portrait orientation only, but if I add such custom image size, it will be created for all of my uploads, including photos and other images that will never need this size.
The standard "Add Media" function in the post editor inserts image with hard-coded image dimensions and absolute URLs including host name and scheme (!)
Need to manually update existing posts content after changing an intermediate image size. Currently I have blog post width set to 750px and have defined a custom image size with that width. If I decided to change the blog width, I'd need to update existing posts because paths to image files in them include the exact dimensions.