The arguments you are using are similar to those used to defend the century series; back then they argued that missiles had eliminated the need for agile fighters, but the Vietnam War's rules of engagement meant that agility was crucial. If one is to defend the F-35, it should be on the basis of its advanced strike capabilities, or other design considerations which were given priority.

Perhaps stealth, unmanned, and/or saturation are the best strategies; I am not sure whether anyone can predict what the outcome of an encounter between such asymmetrical adversaries will be in 15-25 years.