I have list down few comparisions, please check.
CATIA CAA API's are made like very small block, so that for each operation we build our own sequence.so it is powerful, But in Pro/E each operation is done by sigle API.
UI development is Automated in CATIA, But mostly coding is prefered for a good one.
CATIA CAA API is COM based, but Pro/Toolkit is library based.
Writing CAA API requires very good skill in Object Oriented programming, relatively Pro/toolkit is easier.
Application compiled in to small small DLL's and finally the entry point is EXE in CAA, but in Pro/Toolkit entry point is both EXE and DLL.
Additional menus are created in ProToolkit, In CAA only toolbutton is used to call back the application.
More structured development environment in CAA than Pro/Toolkit.
More API's are opened in CAA for functionalities than Pro/toolkit.
Development is more faster in Pro/Toolkit than CAA.
Automated code development is available for CAA.