A bit busy right now. I'm gonna post something here to explain how I think it'll work, and why we probably can't use mespirit. Give me 30 minutes or so.
Okay! I'm back. So, lemme point some things out. Doesn't Hoopa's regular form have base 600? That makes it viable. Secondly, the difference between this and insurgence is the fact that there's no prophecy, only one cult, and they're hunting for the pixies for a completely different reason than the cults in insurge.
Insurge cults want to destroy the pixies and their chosen to preserve themselves. BN wants to hunt the pixies for their own gain.
The way the pixies work is they each follow a theme. It's a choice between emotions and elements. Either way they will be divided into separate sub-regions(Forest, Spirit, Mountain, Frost, City). Both Shaymin and Celebi cannot be used at the same time for this reason. If you go back a couple pages, since I don't have the time to re post it here, I suggested that if we use the elements theme, we go with Shaymin due to it fulfilling the Sky component. If we go with emotions, I suggested Celebi, due to time/age= wisdom. Try looking around page 23. Hoopa, in both instances, fulfills the "Spirit" component.
These Pixies, with Mew as the catalyst, will be the keys to breaking the restraints on Giratina or something. That last part hasn't been worked out yet.
Now here's why Mespirit won't work. If we use Mespirit, we need to use the other two in the trio, or else it just doesn't make sense. Keep in mind that whatever we do to Mespirit, we'll have to alter the entire trio.
But that brings up the point that it's a trio, and there are four sub-regions (five if you include the central city). In addition to this, Mespirit, Uxie, and Azelf are the keys to controlling Dialga and Palkia, and have nothing to do with Giratina and the BN's goals. It's also ripping a few pages right out of the Gen 4 games.
The too many legends thing can be alleviated if the story/region is long enough, which it seems to have the potential to be.
Edit: more detail added. Also check page 23.