Designing a custom button in Photoshop is easy — that’s the part of the iceberg we can all see. Below the surface it takes a lot of effort to get the details right: building pressed and inactive states, preventing text highlighting on double-click, adding right-to-left support, testing accessibility, and so on.
I often hit this iceberg when I stray from native controls. For example, Ajax interactions require more polish than basic web pages. Custom mobile menus require more polish than the built-in version. If the team doesn’t have the time to polish custom UI, it’s often better to stick to the boring native controls that work.
Custom controls can really add to the experience, but they're not cheap. Buttons are one thing. Dropdown menus are another. If you have to do it, libraries like Nathan's Formalize are a great head start.