Why use PLC instead of microcontroller?
The higher cost of PLCs is offset by the testing (often in nasty environments) they are (or should be) submitted to. Could you design a custom microcontroller system? Yes, but then you'd probably need to certify it. 

Customizability is not really a major issue when you have a large plant full of equipment; in fact, you want the opposite, you want stuff to be as standardized as possible. 

Also, ladder logic is already pretty much standardized &mdash; except for vendor-specific features &mdash; which make debugging/porting software between PLCs a simpler task than it is porting between different microcontrollers.