Well, the theory is there was only one true generation of 9000 (minor redesigns aside). So when they redesigned it they wanted to make it known and out popped 9-5.
Meanwhile, there were two generations of 900, and for the third they renamed the car 9-3 to coincide with the new 9-5 name. None of this is true, by the way.
You know what I find odd? The 94-98 Saab 900 was the same vehicle as the 99-02 Saab 9-3. Correct? Yet the 98-_ Saab 9-5 is completely and totally new (or, it was in 98 and could be bought new today). So why the hell does the first-gen 9-3, which truthfully debuted in 1994, look and feel ages newer than a CURRENT 9-5, which is still being sold at dealers today!? Does everyone agree that among Saab's two 2002 models, 9-3 and 9-5, the 9-3 was the more forward-looking?