[Alastor Mobius Toth]

It wasn't a Super Hornet, it was a Tomcat.

Well, being outdated doesn't preclude something from being used; in ML Soviets still use the outdated MiG-23s and -27s, simply because they can't really replace them with MiG-29s and Su-27s. Incidentally, Tomcats are not considered to be outdated by the US (at least in Comet), it's performance is still within the acceptable range of current-gen TSFs (especially the -D model), but there are simply other constructions that can do the same at lower price, hence Tomcats aren't being made.

Not much actually. Canon!M-L economics are actually pretty wonky; irl a wing a battalion of Raptors like Hunters would cost enough to bankrupt a small country, but M-L America is implied to be able to replace most of their older machines with Raptors. In same vein, Soviet Russia in Muv-Luv should not be realistically able to replace the losses in the TSFs, given that they have virtually no resources under their control, and it's doubtful that they could move many factories to Alaska.

It's a bit of a moot comparison, since Active Eagle is a tech demonstrator, and most likely wouldn't be used for mass production. At any rate, Silent has the advantage of Stealth, but Active has more SPPPEEEEDDDD. Avionics wise, they seem to have the same 3rd Gen equipment as other American craft.

Also, I should set something straight right now: Comet is a M-L AU, and it doesn't follow M-L world to the letter.