I realize this answer comes VERY late. But I ran into this post and figured one answer to the question could simply be: "Why not have both?" (eat cake and have it too) and also "Why expend the effort on implementing both when I could just expend the effort for one and get the second one for practically free?"
Toward that end, I present an Inno Setup script w/ MSI support:
https://github.com/cubiclesoft/php-app-server/blob/master/installers/win-innosetup/yourapp.iss
There are some custom Pascal functions in use here that kick in when passed /MSI={GUID}
on the command-line that trigger useful changes to the script (e.g. no Uninstall icon in Start or Add/Remove Programs).
And I present a WiX script w/ support for the above Inno Setup script:
https://github.com/cubiclesoft/php-app-server/blob/master/installers/win-wix/yourapp.wxs
The WiX script wraps the Inno Setup-based installer EXE (the only payload) in a way that triggers the Inno Setup script to do things in a more MSI-compatible way and cranks out the MSI. It isn't perfect, but it saves a ton of time by letting you do things the Inno Setup way and then get most of the benefits of MSI (e.g. GPO/SCCM/DSC silent deployment) without pulling hair. This works best if mostly just deploying files to the system and a handful of registry entries (i.e. a basic app). I wouldn't recommend this approach for a larger application where there are lots and lots of components, but if you try it and it works, let me know! Having a MSI version that launches the Inno Setup EXE at least gives sysadmins doing deployments something reasonable to chew on.
Note that the WiX script depends on the custom Pascal functions on the Inno Setup side of things. You can't just take any ol' Inno Setup installer and wrap it with the WiX script and expect it to work (it probably won't). But maybe a future version of Inno Setup will natively support something similar.