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I'm just thinking here, but I feel like the whole concept of the Great Barrier Reef has been under-hyped. So far. That's such a huge part of Australia and it provides a lot of potential for the villain groups.
>Group concerned about money is overfishing and destroying the Reef
>Group concerned about protecting the environment goes psycho and builds a fence around it
I especially like the idea of the second one. Let's say that this group goes crazy and builds a fence. The gym leader's daughter gets sick and you need to get into the reef to extract medicine from one of the unique pokemon that lives there.
It gives you an excuse to fight the criminals and a plot for the villains. We could also utilize some sort of Kraken pokemon. It doesn't have to be legendary, but have a Gyrados-theme when something retarded like an anemone evolves into a multi-tentacled kraken.
Also, anemone pokemon would be fun. And urchin pokemon. They could be like the zubats of the reef.