At the risk of repeating myself from the last time this question came up, let me selfishly say as a NTP maintainer that I do not look forward to NTP configure failing with a message indicating GNU make is required and could not be located. I have no appreciation for how much simpler and easier to maintain Automake might become with a shift from targetting portable make to requiring GNU make. I've never maintained Makefile or Makefile.am files in a GNU-make-only project. I do find it is sometimes easier to track down problems affecting both GNU make and more traditional implementations using a traditional make as the verbose debug output of GNU make is so much longer due to more implicit rules.
It would be my inclination to stay with older Automake as long as feasible if newer Automake drops support for traditional make. Harlan Stenn, who initially converted the NTP code to use Autoconf and Automake, likely has a different perspective which might well matter more than mine. Cheers, Dave Hart