I don't think the GE is flawed in that regard.
That's really how it should be. Jack of all trades type players are nothing more than niche players in the NBA, truly elite guys are spectacular in certain areas and not so great in others.
If a team has a C who is a monster with 20 IS and 20 RE and 20 ID, it would be inexplicable for his counterpart to outplay him just because he had better shooting range and was a better ball handler.
One well rounded player will not beat his monster counterpart in this game.
However, a team of well rounded players can be better than a team of monsters, because they become more than just the sum of their parts.
"Air is beautiful, yet you cannot see it. It's soft, yet you cannot touch it. Air is a little like my brain." - Jean-Claude Van Damme