The thing about app installs is that if you don't abide by ms's "suggestions" things will be more tricky.
For instance, ms says to install stuff under \program files\YourApp, but after the install, you aren't allowed to WRITE into the program files folder at all. All prog data should go either in the current user's APPLICATION DATA or the ALL USERS\APPLICATION DATA folder. For commercial apps, that makes sense, but for something like Mala, that'd be a bit of a pain. Generally, you want Mala to be installed in a specified folder (say c:\Games\Frontends\Mala) and for all it's config files to be right there in the same folder. Problem is, if the user does that, THEY have to be aware of permissions and be sure to put mala somewhere where it will have correct permissions according to the user's credentials used when Mala is run. For instance, I might install Mala while logged in as "JoeBob", but I plan on using autologin as "Guest" with limited permissions when my cab normally starts because I don't want game players to be able to start up explorer and go traipsing through the filesystem.
To make that seamless for users might take a few minor tweaks to Mala to vector where it's reading and writing it's config files. But then, I might be complicating the issue here. Maybe the common problems are simpler than that?
I'd be happy to help out if you'd like. I've done A LOT of installs over the years, mostly with WISE or Installshield, but I've used InnoSetup a few times too.