I updated my installer from ISE 3.1 to 3.5. ISE 3.5 now uses Windows Installer Services, and that is where I ran into problems:
(1) WIS allows no more than one install of a product on a machine. It is not possible to set up a "training" install and a "production" install on the same machine. This is astrategy that many of my users follow.
(2) To reinstall, a user must first "uninstall". So when a user goes to install, he sees the "remove" dialog. My users found this very confusing and a great number of tech support calls ensued.
(3) There were some unusual situations that WIS did not handle gracefully. For example, if the TEMP variable on the install machine pointed to an invalid address, the installer stopped, then tried to finish the install each time the user rebooted. Again, confusing.
(4) WIS often needs to be updated itself on the end user machine. You must allow the reboot after this update or the installer fails.
(5) WIS often generated silly, misleading messages that confused the end user and resulted in extra support.

I am going back to ISE 3.1 which worked flawlessly. FWIW.