I inherited a handful of InstallShield (v12) projects. The files are all text/XML and thus there are no version control issues. We have a build machine that uses their command line tools, which works well. What I don't like is (a) the cost per developer seat and (b) bugs.
Inno Setup is very capable/flexible and there are generally multiple ways to accomplish a goal, which led to a steep learning curve. We are several versions behind their latest version (due to their upgrade cost structure). Because our products run on Widows, if we have to switch I might first research Microsoft's installer solution that comes with a MSDN subscription.
