With most patents, the company that developed the technology to be patented has a unique advantage even without the patent. They have a better technical understanding of the technology than the competitors, and they can incorporate it into their products faster.
With crop patents, the patent seems far more necessary as an incentive to innovate. If Monsanto can't patent their new seed, then anyone else who wants to can also sell the seed, and Monsanto will never recoup the R&D costs. Under this scenario, I don't see why anyone would develop new plants.
Assuming we want to encourage selective breeding/genetic engineering of new plant species, what incentives can we devise that don't have the problems posed by patents?