Aquaponic systems can be more difficult to set up than hydroponic systems, and growing fish is added cost. You'll need to create the ideal conditions for both plants and fish.
Hydroponic system relies on chemical nutrients, while aquaponics uses fish waste. Although the latter is much more organic, it can be tricky to properly regulate pH.
Hydroponic systems can function without growing media, while aquaponic systems require a root system in soil-like media for beneficial bacteria to live and convert fish waste to nutrients.
The hydroponic setup only considers the optimum pH range of 5.5-6.0, while aquaponics must simultaneously consider both pH levels for the plant and fishes.
Plant growth in hydroponic farms is faster than in aquaponics because the nutrient solution is optimized for the crop needs. Premix solutions can be bought for specific crop needs.