He had been given little incentive to learn to use it better. Surely SHIELD could have made a project of him and found a way to enhance his natural ability much like the Extremis did. Why was it necessary for May to inject him with the Extremis then? It was her double-dose that set him off. He is a human who is both fireproof and able to create (and control) flame from his hands. Limited or not that isn't someone you let walk around unutilized in a world where Captain America, Hawkeye and Black Widow are considered superheroes. Who says Extremis was even the reason he was able to perform at that level? How would they even know that his powers would be enhanced? It may just as likely have been a mental block from a lack of confidence and the discouraging warnings of SHIELD. This is the most powerful naturally occurring (not engineered or the result of an experiment gone wrong) meta-human ability we have seen in the MCU. I just don't buy it.