I also posed the same question on use.Perl. I got a selection of opinions there too.
There are advantages to Module::Build, in particular on platforms without compilers, e.g. Windows and it will apparently become the "standard". However the traditional method is more tested and far more common.
In my case I just need to fiddle with the Makefile.PL and make it add optional tests. Basically I need a bunch of modules to test the code, they aren't actually need to use it, so I don't like making them pre-requisits if I can help it. I prefer to use Module::Build, it is easier for me but I'll have to maintain both...
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