Because the USAF are dopes when it comes to naming conventions. Some they get are great, Eagle, Raptor, Raider. Then pull stupid crap like B-21, F-35, anything "II" in it. The latter inevitably gets a nickname from the front line guys.
The reason for the F-35 being the Lightning II was it also translated well for all of the other air forces using it. Also the P-38 built by Lockheed and the BAC Lightning. Yeah, it's stupid marketing, but marketing usually is. You note in your paragraph that the Raider is a great name and then say the B-21 has a stupid name. You really need to make up your mind.
Although, what I think you're trying to say is the designation system, not the name. Aka B-3 instead of B-21. Once again, marketing. As for the F-35, I think they did what they did because there are reports that a YF-24 was flown and if they had followed standard convention, the F-35 would have been the F-25. Then everyone would be asking what happened to F-24? The collective shrugging from the USAF would have been more laughable than simply saying we're going to change the X to an F.
The one that was stupid to me was "Fighting Falcon." I know they didn't want to call it the Viper because of BSG, but the pilots call it that anyway. Although, now they try to claim it's because the YF-17 was named the Cobra, which is complete bullshit. I remember AvWeek quoting the USAF saying they weren't going to name it after a sci fi TV show fighter back then.
Of course they're program names are even dumber. Go look up, "Soaring Otter." Soon to be followed by Swimming Centipede and Gloating Wombat. OK, I made those last two up.
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