Problem is that when you go down that path it's difficult to know where to stop - A citrix install is easy for some things and extremely difficult for others, macs, bsd's, mobile phones are other examples. Again, using the MSI example, surely copying to a remote fileserver and placing links is easier than an MSI deployment - so why weight an msi install over a manual filecopy.
Agreed that there are may different types of systems around but they could be assessed against what they are supposed to work with. For example if it is windows software it should run with MSI and not write rubbish everywhere. If it is designed to run in linux it should be packaged or a simple case of unzipping it rather than spending half a day tracking down, installing and troubleshooting all of the dependencies.
Designed for Windows XP/Vista Windows criteria
Designed for Linux base Linux criteria
Even if you don't have an AD backend the fact that the MSI has been designed to be automated and installed silently via GP means that the install can be triggered silently and successfully via a login or autoit script provided by a linux server.