I would add several more points, but these can hardly be called serious limitations since they all can be worked around:
- There's no ready-made tool to embed transforms (MST) into the MSI package; this is where msidb.exe comes to the rescue
- You have to do extra work to create a single package with a number of localizations, like creating N packages, generate N language transforms against a neutral package, embed those transforms into the package, instruct your bootstrapper to call correct language transform
- WiX 3.0 has rather limited IIS extension - it supports IIS 7 only in IIS 6 compatibility mode; but fortunately this is no longer true for WiX 3.5
- Heat can't generate "1 component - N files" by default. Yeah, I know, it's not recommended, but sometimes you need it; fortunately, you can transform the heat output the way you like with XSL
- PermissionEx of UtilExtension doesn't have a switch to set ACLs on folders only. If you need to set ACLs to your installed files only, this is quite minor. But I had to patch WiX with a quick fix to be able to say "apply these permissions to folders only" on existing file system tree
Again, let me repeat that I don't consider those serious limitations. I'm very happy with what Rob and the team have done so far, and they are on a right track! :)