The argument for JC as GOAT seems to me to rest on two propositions, which inter-relate.
First, that he is the greatest "program builder" of all-time - that he scrapped, and out-worked, and out-hustled, and out-coached to push a former non-entity to the highest level of college basketball, whose achievements now rival those of the closed coterie of the sport's traditional royalty (yay, I almost avoided the term "blue blood."). On this view, we can emphasize some of the particular strengths of his legacy ("doing more with less," i.e., winning with lesser recruits and developing the best NBA talent) and explain away some of the inevitable shortcomings that appear on his resume (inconsistency from year to year; his relatively high career loss total - he built winners at NE and UConn, but you have to break eggs to make an omelet; etc.)
Second, that his accomplishments in the tournament - having come in the "modern" 64-team tournament era - deserve somewhat greater weight than Rupp's or Wooden's. This is not to say that 3 "modern" NCs at Cowtown U (or 4 at Tobacco Road U) are better than 10 "classic" NCs, but just that the comparison between eras is not exactly apples to apples.
Just my 10 cents, as to the admittedly tenuous case for JC as GOAT. (Nor, obviously, did I offer the Hoosier case for BK, which I imagine would emphasize things like "innovator," coaching lineage (helped spawn another GOAT candidate in K), undefeated season, Calhoun-level badass, etc.)