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At first they were going to follow the storyline of the original AVP comic but it got scrapped for budgetary reasons I think. Shame because that would have been cool to. I never liked that Pred-Queen hybrid idea, it had already been done in AVP Extinction as the Final boss of the Predator Campaign. Plus that queens backstory was that she was a bio-weapon created by a mad scientist along with the yellow K-Series Aliens. I'm also not a fan of that Predalien design, personally I prefer something like this. Pred-Queen Boss K-Series Aliens Bonus Berserker Alien - Super Predator Host

I think you're expecting a little too much from a medium that regularly features super powers/giant robots/magic all being used by preteen girls. Especially when poorly or truthfully portraying Middle Eastern people sometimes comes with Death threats that aren't just rabid fanboys. That and it's probably not something they think is popular right now. Japan creates Anime for the Japanese, and nobody else. If they don't think that is a popular subject, they won't make anything about it. The times where you see it, it is usually used as a reasoning for: 1. Quick and easy bad guys. Everyone knows they have extremists and usually doesn't require much explanation; or 2. Quick shorthand for maladjusted young men to have combat skills and a stoic/violent attitude ( see FMP! and Gundam 00)... But in a lot of cases you'll also find that they are still oddly Japanese in some aspects, and not 100% middle eastern descent. Sure, occasionally we'll get a high quality anime with some aspects that really stand out... But those are few and far in between, and by the law of percentages, rarely ever deal with Middle Eastern issues ( again, cause Japan does Japan)