Manarex you have said your sons setup' sounds not too bad with bad speakers, so the conclusion I come to is the much better M60s now require a much better sub to come up to the same quality and a more powerfull amp would certainly help.
Your friend you mentioned that swears by Polks might consider the big boomy/muddy sound to be better as many people do feel this is the way a sub should sound. I have a boomy muddy sounding Sub and after hearing some much better quality sub, EP600/EP400/HsuSTF1 the Polks/Paradigms and a few others in the stores are not quite in the same league for the same price, IMO. I am now aching to get an EP500 or Hsu.
If you are not happy with that sub I would certainly take it back if you can, no use paying for something you are not happy with, then put that money towards another and try again.