They let more particle contaminants into the engine when compared with paper filters.
They're dependant on the owner to dutifully clean and recharge the filter for maximum efficiency.
They can potentially wreak havoc with the mass air flow sensor. FWIW, the owner's manual of my mother's new Mercury Sable specifically warns that use of oil-impregnated air filters such as K & N will void the engine warranty. Definitely avoid using K & N during the warranty period.
In the grand world of engineering design, there is no "best". There is always a compromise or trade-off, even if it's just cost.
95 E320 Cabriolet, 131K