This first half of this year Configuration Manager 2012 will be launched with all the features like discussed here, here, here, here and here . But also software developers around the globe are developing solutions that will bring extra features for Configuration Manager 2012. One of the developers is Roel van Bueren, he is developing a product called Setup Commander.
The Setup Commander will assist you to create Applications in System Center 2012 Configuration Manager and MDT. From what I see is that the Setup Commander will read the MSI and supply you application details to be able to create an Application in Configuration Manager 2012. Configuration Manager 2012 also has the ability to provide application details but I see some nice additions like selecting options to install.
See yourself the first results of the Setup Commander are here.