I'm not sure what would make it too complicated for the average/inexperienced user. The creation of the serial number and the choosing of the folders would be done automatically, with the option for advanced users to modify the settings (by clicking a "Advanced Options" button). Advanced users, by definition would know how to use the advanced options, and inexperienced users really wouldn't do anything different than they do with the current installer (or while using the program).
I'm reminded of a quote:
<tormy> hey when u burn games in discjuggler, under the advance tab... should the block be 2048?
<DCBastard> leave the advanced tab alone
<DCBastard> if you were advanced you'd know how to use it
The problem I see with using the -r switch is that anytime you create a new shortcut, you will have to figure out the switch parameters again. Plus, if you happen to want to run mirc.exe directly, you will not be able to do so.