Presently it has become a standard practice of the web designers to customise WordPress Themes as a part of website designing. However, there are several drawbacks of doing so.
Profound customisation cannot be done on ready-made WordPress Themes
Minor tweaks are quite possible on WordPress Themes. However if one is expecting a lot many customisation, that may not possible on maximum themes including even the most popular ones, as authors set their own limitations for modifications.
Modification limit cannot be set
Modifying a theme can mean an infinite number of changes from the client. Estimating the time limit for completing these changes can be difficult and the web designer might need quite a lot many days to implement all those modifications to themes. In pursuit of implementing originality to an already existing theme, sometimes the total time can exceed to that of creating a custom design from scratch.
One particular theme is often used by several websites. Some websites modify and use them and some use them as is. Therefore, your website does not bear the unique design or style as it may have been used by others and will be used by others in future.
It gets complex to update the website in future
The authors of the themes roll out regular updates in order to keep abreast with the latest updates of WordPress. Therefore modifying the main theme may not be a very good idea as customisations might be lost at the time of modification.
Having said this, it is not that one should not use WordPress Themes to build their website. There are numerous Themes available for WordPress Website Design and some of them are quite good as well. The only thing that you need to keep in mind while using these themes is that the author has already envisioned a particular concept and when you are viewing a theme, you are viewing partial reality of your own website. Therefore, you have to choose a theme that is highly relevant to your website concept and structure so that it does not require a lot of customisations.