For one, there is not enough technology to improve faster and efficient productions of PHBs. Current methods are very costly.
The environment of the bacteria must be kept and an optimum temperature.
The quality of the product may be inconsistent and the variable patterns of supply will mean price fluctuation and the material itself is rather brittle. Land degradation must be made way to produce the sources for biopolymers as well if demands reach high. Even if biodegradable plastics start to be used now and broadly, waste will not completely disappear. Land-fill sites are infamously bad at enabling anything to degrade. Paper itself lasts decades. There are not enough bacteria because there is not enough oxygen around for them to thrive. Large-scale composting facilities will be needed and these cost money.