In a nutshell, applications requiring strength and low levels of deformation would usually employ PEEK, whereas those requiring resistance to voltage or chemicals utilize PTFE.PTFE also rates highly in that it is self-lubricating. This makes it a preferred choice in high wear applications.
The biggest disadvantage of PEEK remains the price. It is roughly 10 times the price ofPTFE and as a result has remained a niche polymer, used only in applications where it is absolutely necessary.