Mmh, I think there's some misunderstanding here. You mean, only select the textures you're planning to use and put them into a .wad, instead of mixing up a lot of textures into a huge .wad file.
Anyway, -wadinclude will still only include the used textures from that .wad, whether it's huge or small. So, you can still use the seperate .wad files, and -wadinclude all of them. The results are the same when you mix these textures together into one wad file that you -wadinclude. My point: why the extra work of putting textures into one .wad file?