Stockton might have been a crappy outside shooter for today's standards in his first years, but there were few good outside shooters back then. Besides, he had a very good mid-range game and was a GREAT finisher around the rim - even in his later years, when his athleticism was waning. Rubio, in comparison, has improved from midrange to the point of becoming good but not great, but it is still mediocre and inconsistent from outside. He is truly AWFUL finishing around the rim, though.
In other words: if the team needs a basket, it can't count on Rubio to get it.
Just check how AWFUL Rubio is from 0 to 3 feet:
http://www.basketball-reference.com/players/r/rubiori01.html#shooting::none
Few players in the league fail to reach .500 from 0 to 3 feet. Rubio has reached that mark only once in six seasons. Truly awful!