Disadvantages for customizating WP without pluggin

Can someone please point out the disadvantages of customizing wordpress without a plugin?

Let’s say an organization wants to build a site with some specific functionality that does not exist in WP, but want to take advantage of built-in functionality of WP such as user registration, content management, etc. and maybe pack this specialized code in a plugin.

The dilema this organization faces is to choose between fresh development or a solid featured based tool such as WP to speed up development.

What approaches is recommended to avoid problems with upgrades, maintenance, etc.

Is the plugin the right approach?

PS: the developer has some intermediate WP PHP knowlodge;

Thanks
Rod