Ultra Forms in Battle Gem Ponies seems to need more attention on this blog. Kinda surprised I haven't clearly explained how it currently works on the site yet. I've stated before that it's a temporary effect that works a lot like mega evolution does in Pokemon. You can get some details on how it works below the break.
Each of the ponies above can use an ultra stone and transform. The only ponies that can't do that are the ones without a class (Neutral ponies) and the 18 different forms of the starter pony. Since it requires an item slot, any pony that only exists because of an item (the starter's alternate forms, for example) can't go ultra.
Like Mega-Evolution, Ultra Pony stats will change, new abilities replace the old, and their classes may change too. For instance, Sweet-Bot's Esper secondary class is replaced with Surge in ultra form, making a Lock-On / Wonder Bolt combo very deadly, as well as give new power to moves like Scatter Bomb. In some situations a class change may end up being unwise, so the player always has to think carefully about when to execute an ultra transformation.
Only one of your ponies can go ultra per battle since it overcharges your pony's gem. Multiple ponies in your party can have the potential to go ultra if their primary class matches the stone's. So if one gets knocked-out you can have a backup. While ultra, your pony can still switch out and when switched back in, it'll still be in its ultra form.
Hopefully this adds more excitement to battles and opens opportunities to bring out the big guns and put the match in your favor. Balancing ultra stones with other battle items will be difficult, but should ultimately result in another layer of strategy. Players will have to choose what works better for their team, an ultra pony, multiple ultra candidates, or a powerful item that can prevent a malady.