Flex/bison are special because they are directly supported by Automake. Cweb is supported in the TL build system via a shell script that handles all issues for parallel make, but still needs special build rules -- Noweb could be handled in a similar way.

From the build system side, I'd think normal users (i.e., people building TL or just luaTeX) should not be required to have either Noweb or Doxygen, as they are not required to have Autoconf, Automake, Flex, or Bison.

Yes, please, no more Gnu/Linux specific stuff for we the poor guys who must work in Windows. So I like CWeb too.