What are the disadvantages of commercial farming?

Water pollution due to runoff from fields treated with pesticides and fertilizers; destruction of wildlife habitat to produce more crops; soil erosion, nutrient and organic matter depletion from constant application of fertilizers and removing portion of plants which contain the most nutrients (seeds); higher demand for crops to be grown for ethanol production and animal feed than human food; high costs associated with purchase and application of pesticides and fertilizers, using fuel for machinery, maintenance and repair of machinery, and labour; vulnerability to market fluctuations; vulnerability to legalities and from suppliers and purchasers (i.e., Monsanto, as mentioned in the TV documentary Food Inc.); "bigger is better" is not always the case; and many others.