I went with Zappa. In a lot of ways, I adore Captain Beefheart, but feel his influence/personality often outweigh the quality of his musical output. Beefheart was a true original, and a genius in many ways, but basically hit his limitations early on.
Essentially, Beefheart had his thing that he perfected for Trout Mask Replica, and polished with Lick My Decals Off, but I think he really failed to go anywhere from there. As ingenious as a lot of the subtle values of his work, once you get past those it's all just basically all just off timed blues with abstract lyrics.
Zappa consistently changed his sound from year to year to year and seemed to have a pretty good grip on what he was doing. He has his great albums, and his stinkers, but he continued to evolve his sound throughout. Beefheart's only attempt at evolution after "Lick My Decals Off" was a failed attempt at a commercial sound for years ended in just a reversion to the Trout Mask Replica sound. (Bat Chain Puller I believe was actually all material written between Trout Mask Replica and Lick my Decals off, Baby.")
Plus, I've never been keen on Beefheart's ridiculous ego, and insane obsession with having to mix the instrument tracks down to nothing so his, admittedly awesome, voice could be heard.
Both geniuses, both innovators, but I feel Zappa is a significantly more poignant musician who would only be overshadowed by Beefheart due to his underdog value.
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