Like all home grown hydroponics system the biggest disadvantages come down to cost - both in terms of purchasing and running the system. Because this system involves near constant pumping of water it uses more electricity than Deep Water Culture passive setups like wicking beds. Using a passive wick for the nutrient solution uses no power at all and is cheaper to run. Pumps, timers and valves also cost money. You can't cheap out - badly made parts kill plants. You also have to watch out for high humidity. The flow of water can result in growing areas that are very humid, especially beneath the leaves. After all the flood tray keeps all that moisture quite low. It's a substantial disease risk for most crops. Lettuce for example is prone to leaf disease and basil is vulnerable to downy mildew. Keep in mind the growing needs of your crop and provide extra ventilation if required.