You're asserting that all opinions are equal, that because there is not a unanimous opinion that an opinion can't be a binding legal obligation -- allow me correct you there. A court's opinion is more important in this case, it has ruled the patent to be without merit. Fines to dissuade further abuse of the patent system are in order.
While systemic changes to reduce the ability for abuse are needed, this isn't a time for better planning -- it's about responding to abuse that has already happened. You don't ignore that and merely lament that you need to better the system.
(i.e. You broke the rules, you receive a punishment. The system is, by poor design, promoting the breaking of rules, you fix it. Both can be true.)
First, they're enraged over a kidnapping, iirc, of their eggs.
Second, it's because the game is about cartoon animals - there's a lot to be said for evoking social issues, like your jihad example. It wouldn't be a 1 for 1 swap.
No problem is so large it can't be fit in somewhere.