If Zappa was still alive I'll bet he could have been president, a real statesman. He had more imagination than any other composer/musician and he didn't bullshit around. I noticed a lot of women don't like his music because of his lurid lyrics and innuendo, sure, taken right to the edge, but still true with a huge dose of humor to boot.
He was also responsible for giving a lot of musicians the break they needed, ie. giving them a chance to work with a master who arranges complicated pieces. They went on to form their own successful careers afterwards. His filmography like 200 Motels and Baby Snakes are masterpieces. I might add that EVERYTHING Zappa did live and in studios was recorded in one form of another. He had huge archives in his basement and was very secretive and possessive about his material.
Saw him twice in concert and he was quite reserved. Kinda funny just seeing him sit on a stool at center stage smoking a cigarette with a cup of coffee while the rest of the band is going apeshit around him (TWO drummers). But when he steps up to play the guitar... WHAM. Just listen to the live cut "Son Of Orange County" on Roxy and Elsewhere and you'll hear what I mean.
I never did like comparing musicians/guitarists, its like apples and oranges. Maybe Vai is the better guitarist (faster, whats "better" anyway?) but Zappa was the better musician and showman, handsdown.