The biggest challenge about WordPress is it’s lack of customization.
Now you may be thinking, “But how does it lack customization, you can literally build anything you want,” and I would agree with that statement for the most part. However, compared to that of HTML and CSS, WordPress just doesn’t have the the freedom that they do. Sure you can do a lot in WordPress but you’re limited to only what the program and other templates allow you to do whereas with HTML, you can quite literally create whatever you want with the added caveat that it is just more difficult and requires more skill and patience to do. Thats the big trade off, sacrificing infinite customization for ease of use.
Another thing to mention regarding the “lack of customization” is that, sure you may have access to a plethora of themes and plugins to choose from, but you can’t just use any one you like willy nilly. Themes and Plugins take extra considerations, such as compatibility with your current version of WordPress, constant updating, and adding too many plugins or the wrong theme can cause your sit to run slower or less effectively.