Advantages are almost limitless, so I'll list disadvantages.
1) So far, genetically engineered agricultural products are still cranked out in genetically homogenous batches that are highly vulnerable once an infectious pathogen figures out how to infect one. I don't think they've figured out that they need to create variation in GM organisms.
2) Unintended consequences; some have blamed BT corn pollen on the disappearance of honeybees, and that wasn't such a bad guess, but they swear they checked and that's not it. Insecticidal BT plants hybridizing with wild weeds would be disasterous to insects, which are a cornerstone of animal food chains. Even the adaptation of insects to BT toxin could be a monumental disaster.
3) If genetic engineering is done in humans, and humans can incorporate "superior" modified genes into their germ line, class differences could be exascerbated whereby only the poor ever get sick, and continue to be the least able to afford medical treatment. The wealthy will get "sick and tired of paying for poor people's diseases," and you can imagine where things go from there.
4) When genetic engineering technology becomes modularized and more widely available, there could be a "911" event in which nobody ever imagined the need for safeguards against the genetic engineering equivelent of insanely violent people putting non-war technology to the most destructive imaginable use.
5) Here's another disadvantage: More perfect medecines could throw natural selection in humans; a highly defective human could be made to appear genetically fit, someone will marry that person and have eight kids with them, and produce defective offspring dependent on advanced medecine; that is, for treatments produced by genetic technology that are not incorporated into the germ line. (An organ produced in a pig, transplanted into a human for example).