My concerns are not only about building the code itself, getting the code compiled into geany.exe and libgeany.dll is easy enough, with autotools, Waf and even hand-written Makefiles.
The fun begins with the stuff around, basically the 'make install' part with all those Windows specials, renaming text files (README, etc.) to *.txt , signing binaries, creating the GTK runtime bundle and last but not least the installer.

If @kugel- can guarantee all this for Geany and Geany-Plugins in the same or better quality than before, then I'd be fine to drop Waf immediately. But if not, we first need to sort remaining problems out.

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