I like ANSYS for CFD/FEA. The workbench interface is very intuitive and the translation in from Pro Engineer is excellent.
You can do parameter studies by naming parameterized dimensions with an DS_ prefix and Pro Engineer will automatically open and generate the next model for you.
Also if you implement EKM then you can use an automated workflow for future studies by even non-trained personnel. I think this is the answer that you are seeking.
Rule 1: Don't model anything using surfaces.
Rule 2: Make everything pass a Geometry Check before any simulation.
Rule 3: If the parts are assembled make sure that they are actually touching each other where you want them to touch.
Rule 4: You should model your parts so it is easy to change the dimension to worst case scenario (i.e. Minimum/Maximum conditions). Don't use created dimensions for important tolerances.