I guess it depends on what you mean by a WikiTree Enhancements Project. Do you mean just people giving their suggestions for the site, or actually doing development?
If it's the latter, then I think keeping it together with WikiTree Tools makes the most sense, because it's going to be the same people.
If it's the former, then maybe separate makes more sense, but then I'm not sure a Project is the best format; that's pretty much what people already do here on G2G. :)
Unless, I suppose, you're thinking of people doing more than just suggesting things, and actually helping work out the details of changes to the site...