Yea it's brought up when people think he underachieved during that time. Trying to equate Slam head to head with how many weeks at #1 you have isn't going to fly no matter how hard you try. One is of historical importance used to measure the greatest and most dominant players of all time, and the other is not.
How can it be flawed when it's based on whether you have more points than everyone else and nothing else? And if we are talking about beating the best players in route to Slams, how many times did Nadal beat Federer or Djokovic for a Wimbledon title? once. AO? once. USO? twice. Djokovic and Federer have more big wins than that en route to theirs so you're not really talking about Slam head to head. You're mainly talking about RG head to head, and sorry none of these compare to weeks at #1.