I had to choose between NSIS and Wix - and while native installer formats were clearly the future even back then, the performance and compression advantages of NSIS were so great that it was a clear choice. Solid LZMA was simply impossible to beat by any deflate/zlib/mszip oriented tool.
The joy of the dev team was palpable, the new installer was about 60% smaller and installed in one third the time.
These days, I would personally use NSIS for small stuff. Wix installer for anything bigger/more enterprisey. Last I checked SharpDevelop's WYSIWYG editor was pretty decent for Wix dialogs.