The F-22 was a pretty radical departure from what came before it, and I think it served as a prototype for all the subsequent next generation platforms from which many things were learned. As good as it was, you aren't going to get everything right the first time and technology progresses.
You might think history proved Gates wrong, but no air power can compete with what the US has now, sans the F-22, and it would have been very expensive.
For example, a war with China, if it happened, would be most expected around Taiwan; how would F-22's reach the fight? There are no airbases nearby, except on Taiwan which would be innundated with missile attacks. The F-22 doesn't fly from aircraft carriers (which are imperiled by China's missiles regardless). The US needs a longer-range fighter in the Pacific, to cover the vast territory without bases.
Also, the F-22 afaik doesn't integrate with the new network-oriented joint force, where every asset is a sensor and node on the network, all sharing and a view of the battlefield. It doesn't integrate with 'wingman' drones, now the concept for at least part of the Air Force, where human-piloted planes control several drones.
Instead, the US spent that money elsewhere at the time, getting a better return on investment, remains in the lead now (with F-35's), is building a bomber for the China contest (B-21's), and designing a new fighter.
True, same with the Seawolf-Class Sub's, just too expensive for the "now"-state. However i think with china, the US has to go back to the far-ahead-tec doctrine....fast...