People have done all sorts of things for wii patches. Wii isos are encrypted as standard so don't use a simple xdelta or bsdiff type patching method on those, if you do then you will likely be including a whole bunch of copyrighted code and your patch will be rejected.
Personally I suggest people target either the individual files and make end users extract them or the fully encrypted original isos. Trying to do for whatever flavour of compressed or rejigged WBFS is a nightmare for both you and the end users should they have a different type of iso.
As most of your users will be on windows you can include a batch file to make the patching easier, https://wit.wiimm.de/
is the common tool for command line wii iso bothering. http://wiki.tockdom.com/wiki/Wiimms_ISO_Tools
There are people which use either hacks or loaders for their hacks, do it if you want or can but I don't think it is an option for you (smash brothers has an unpatchable hack built into it so some in that game modding scene use it) unless you want to chain it with a hack.