Think about it, the reason they weren't used and its an obvious one,
The movie would have ended in a mere 25 minutes, Do you really think Tempest and the Storm King could have taken Ember, the Lord of the dragons and her army? Or even better, A Dragon-Changeling coalition army? Prince\General Pharynx is the best at strategies, add that with the Mane 6 and The Storm King would have not only lost his entire army, but he and Tempest would have been easily captured.
So I see why they decided not to use them