This looks interesting. I will offer my two cents here and say that you should make the crystals physical implants. Like you use them but they graft onto your body at skin level. Maybe at Chakric centers or some other place. Then limit just how many a player can have in them at one time, and put limits in so they can't just change a crystal out whenever they feel like. Make them suffer exhaustion and have to rest or something along those lines.

As for the company, if they can do that much, the question is how? Do they also use the crystals? And if not, then are the crystals enough to overcome whatever it is they do use?

See that's the problem with godlike antagonists. They are either unbeatable, or must be nerfed illogically in order for the players to win.

EDIT: For placement, make it random. Have some in the safekeeping of the antagonists, and others scattered. Because lets face it, the chances of these things staying in one place for too long would probably be very low, unless said antagonists are [I]extremely[/I] good at what they do.

EDIT 2: As for sandbox or limited, honestly I don't know. Sandbox could work if you allow new players to seek after the crystals used by the old once said old players leave or go inactive, but on the other hand it allows for posting to slow greatly since the plot doesn't really need to be focused on.

Because sandbox.

If you go limited however, and make the goal getting the crystals and overthrowing the antagonists, then the roleplay itself probably won't slow, especially if you have a reasonable time period in which you expect posts. Then again it will need a definite end, be that good or bad, and it would prevent newcomers from joining once it's over.