Also, sorry for three posts in a row. But a quick look in legends mode seems to indicate why no pokemon megabeasts are attacking. It's because they're all dying off. I think they are just pretty underpowered. I think they need to be buffed quite a lot.
I ran two different generations, with beasts set to very frequent and history set to normal, and in both cases all but one pokemon megabeast was killed off by year 250, and most were already killed off by year 125.
Also, one more suggestion, possibly relatedly. I think you need to buff the size of pokemon. Snorlax, for example, has a size that is half of a Water Buffalo, yet its weight listing is higher than the average water buffalo.
Size is probably very important for the survivability of megabeasts, so maybe you should take some liberties and also buff their size possibly beyond what you might expect, so that they tend to live longer
EDIT: Ooh it hurts to see a Mega Mewtwo Y basically instantly being killed by an elf of all things.