well for one thing the gall carboy is non porous and you don't have to worry about oxidation but they are heavier and break when dropped. the plastic water bottles are going to allow more oxygen to penetrate which is not much of a problem during fermentation because of all the CO2 that is being produced but can be a problem during aging. the plastic bottles are easier to scratch and therefore have a slightly higher risk of contamination. if your interested in using a plastic carboy i would suggest getting a "better bottle" they have a low oxygen penetration and would be fine for primary fermentation.