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Given a supernova with stellar mass $M$, is there a theoretical method to estimating the isotope yield? If so, what processes are taken into account, and how accurate can the estimate be? Would it be more accurate if more properties were known about the star (e.g. metallicity)?

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You have to run a massively sophisticated supernova simulation to get that kind of data. Whole research groups work on them. The biggest unknowns are generally the details of neutrino physics. This is both because neutrino hard data doesn't come easy, and because solving the radiation field of a supernova is a function of seven or eight variables (x, y, z positions, two angles for direction of radiation propagation, energy band, polarization, and time). Trying to obtain decent resolution in all of those variables quickly becomes computationally explosive. Try Google Scholaring "Supernova Yield".

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...and the yield is exactly where your simplifying assumptions are going to make themselves known first. –  Andrew Jul 20 '11 at 19:11
Thank you for your answer, but what were my simplifying assumptions? –  voithos Jul 20 '11 at 20:25
I meant your as in "one's simplifying assumptions." Polarization seems to be ignored in all the schemes I've seen. Only state of the art neutrino transport codes treat angles of propagation fully independently, in a scheme called discrete ordinates. This produces "sunray" artifacts (like a child's picture of the Sun), which are considered superior to the "ringing" artifacts of the last generation codes. The most primitive codes use pure diffusion, which smears particle transport in every direction. –  Andrew Jul 21 '11 at 10:52

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