There has never been an unflawed player, but maybe Hakeem gets the nod for fewest flaws ever? For a center he was damn near everything you could want. Only thing I can really think is that he wasn't a Walton/Draymond/Jokic-style distributor out of the high post - he could find the open man when double-teamed effectively but he wasn't quite an elite passer on the same level as the best passing big men.
That's really fukking nit-picky though. Here are some other nit-picks for great all-around players:
Magic: Exploited on defense, inconsistent jump shot
CP3: Too short and not athletic enough to score at the rim easily or create his own shot against a defense focused in on him
IT: Limited outside shooter and inconsistent scorer
Kidd: Poor shooter and limited scorer during his prime
MJ: Inconsistent 3pt shot, exploited on defense by quick guards who could shoot
KB: Took ill-advised shots on a frequent basis, inconsistent effort on defense
LBJ: Below-average FT shooter, inconsistent outside shooter
Bird: Limited on-ball defender against more athletic 3s and could struggle to score against elite teams
KD: Often failed to take over games when necessary (though less so this year), limited defender unless surrounded by other great defenders
TD: Could be forced outside where his efficiency was inconsistent
KG: Never dominated as a scorer down low
Admiral: Often failed to put points on the board in the playoffs
Shaq: Limited range as a scorer, awful free throw shooter, sometimes poor conditioning
I didn't include old-school players like Big O, Walt Frazier, young Kareem, etc. cause I just didn't really see them enough to pick holes like that.