I certainly think that WiX is the way to go.  WiX bundle.exe with a custom BA
(or WixStdBA and possibly a bafuntions.dll) and external packages staged for
web deployment, is a very flexible framework.  A wix bundle can be an
'addon', 'upgrade', or 'patch' to an installed wix bundle (and the packages
in the "fix" bundle do not need to be msp packages).  So in one situation
with a large legacy (InstallScript) suite setup, which I have not fully
converted to wix/msi yet, I inserted a Wix bundle into a new release of the
legacy setup, which it installs silently as part of that suite of products. 
Now at a later time I can create a "related" wix bundle and release it as a
small downloadable 'Fix' or 'addon' with a new feature.  It then becomes a
part of the original legacy suite (the inserted bundle), and if that suite
is uninstalled then the 'addon' is also uninstalled.  If when the 'addon' is
installed, it registered to more than one already installed wix bundles then
the wix framework reference counts the dependencies and only uninstalls the
'addon' when all registered bundles have been removed.  So all of this
'complexity' is handled for you by the Wix Toolset.  When using the Wix
bundle, you would customize as needed the BA to detect, display UI, and plan
the changes, and then use MSI Properties to drive (headless) msi packages to
do the actual system changes.  Depending on how the web deployment is
implemented, an atom feed is typically used, and therefore an application
could check the feed for updates.  There is good work being done by Jacob to
extend this concept and make the framework even easier to use. 



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