I think it's great for the users, if you are willing to do it, but be careful because if someone complains about installation problems you'll have an extra variable to consider ("did you use Makefile.PL, or Build.PL?").

Perhaps something that you can do is use a templating system to generate both Makefile.PL and Build.PL from a common source so that you only have to change things once. :)

Update: After looking at things in more detail, I see that perhaps you don't need to use templates at all. Module::CoreList autogenerated its Makefile.PL by using Module::Build::Compat with the create_makefile_pl => 'traditional' option in Build.PL.