For me, if the module is a straightforward Perl module that just needs to be installed and have few dependencies, Makefile.PL is the way to go. As others have said, both are around and here to stay, but older versions of Perl are also still around, so compatability with older Perl and core modules is a consideration. There are probably also veterans who still haven't heard about Build.PL and might be confused if a module arrives without a Makefile.PL. Whether these are important considerations is up to you.

For anything more complicated, I use Module::Build. It's a personal decision because I don't know a whole lot about Makefiles. If I want something complicated to happen, it's easier for me to work with Module::Build and make it happen using pure Perl and subclassing. That extensibility using Perl is what makes the decision for me.

If you happen to know a lot about Makefiles, that may not even matter to you.