Y'know, when I first saw the Mystic Theurge, my first thought was, "THEY'VE GOT TO BE KIDDING!"
After I thought about it and read this thread, my second thought was, "Aldric Greymoon can live again."
In a long-ago 2nd edition AD&D campaign, a friend of mine played a grey elf cleric/mage named Aldric Greymoon. Aldric was low on hit points, terrible at combat and armor, but MY GOD, he could cast spells! Using the old 1st edition rules on Spell prep times, it took him a complete DAY to retrieve all his spells. (something like 22 hours at 6th level.)
With 3E, Aldric's character would be reduced to a pale shadow, having to split caster levels, and would not be a workable concept unless the levels were heavily skewed one way or another, and then the concept was adversely affected.
With the mystic theurge, the concept of the 2nd edition multi-spellcaster has been recreated.
Yes, crunch has begotten flavor. But this is nothing new. Many people see "crunch" and "flavor" as mutually exclusive, but the fact is that these two types of play have been feeding off of one another since the beginning, people have jsut been emphasizing one way versus another. I have had grappling rules become the basis for inspired drama, I've had random magic item rolls become the basis for an epic campaign, I've had a single magic items become the inspiration for a small nation of good humanoids, whose start was a helm of opposite alignment. Whereas a character concept was stifled during the rules change of 2nd to 3rd edition, it is reborn in 3E revised.