WiX's biggest issue is the lack of documentation. I actually quite like WiX because of some pretty good tooling (like heat to create WiX definitions for files to install, or dark to reverse engineer MSIs). Custom Action DLLs in C++ are pretty straightforward once you learn how to do them.

However, I found the documentation to be completely terrible. Changing a default dialog required copying some templates from the source branch. I had to search all over Google (and mailing lists) to add a Custom Action DLL to augment the installer functionality in a WXS file.

Overall, I like the text-based format and UNIX-y command tools. However, the lack of good support and documentation is what drives the sharp learning curve. I suspect that the need to produce MSI and desktop software is somewhat becoming a niche.