First of all, this is an excellent idea! I love both vim script and module versions (haven't got the chance to try it, but I will). As for the sequence of functionalities, I'd like to suggest to provide an option to not running the number 4 & 5 (makefile related), as some people writing modules already have a Makefile in their structure, specially if the skeleton was generated with h2xs. I'm talking about the vim script version, as for the module version I believe it is (or can be) more flexible.
I also don't know whether the vim script version requires vim to be compiled with perl or not.
Open source softwares? Share and enjoy. Make profit from them if you can. Yet, share and enjoy!