My take on the setup assistance is to be used only for quick lab test or PoC, and not as a shortcut to setup production and avoid learning ISE properly. The reasons being it creates a lot of config for you from the input info (good) but people may not realize where they have been created and why, and not know how to troubleshoot when things do not work (not good), which will forces you to spend more time back-tracing (or call TAC). You might as well create everything manually, which does not really take that long to get things going, and know exactly where things are and have complete control on all the naming convention.