I think if you're going to use a generator, then what it does should be very minimal; i.e. it probably shouldn't create a complete project. This isn't true of the generators I've seen, which make a lot of assumptions about how your application works so that they can create a minimal working project. This makes sense, because a generator that only half generates a project probably wouldn't be too popular, and would require you to know what's missing. The issue though is that at least some of the assumptions they make are not ideal, and you end up having to refactor the generated code right away; which in my mind defeats the purpose of generating it in the first place.
This doesn't mean that some form of scaffolding isn't useful, since there are some basic commonalities between most of the projects you create that utilize the same frameworks and tools. My suggestion would be to do as @lichtjaeger suggested, and make your own generator. Yeoman generators are fairly straightforward to produce, and you can get some basic scaffolding for what is repetitive in your projects.