Why ? Is it because they got an helicopter named after them ? If so, it's pretty much irrevelant, almost facetious !
They were both plain indians and a cavalery people but only one achieved a major victory against the US at little bighorn.
Well, Apache just sounds cooler IMO. But other than that, in games like this (Age of Empires III) I feel the Apache are underrepresented, much like Siam or Songhai