For starters, I'd spend a lot more time building up the Storm King to be a credible threat. I'd have the party at the start go off without a hitch, and then start showing storm clouds beginning to gather over Equestria, clouds that the weather ponies can't seem to keep away. I'd then have Celestia and Luna explain that, a thousand years ago (because everything is always a thousand years ago in this franchise) they fought the Storm King and managed to exile, but not truly defeat him. His return now could spell doom for Equestria, but it's possible for him to be stopped through the use of a powerful magical artifact, only known as the Eye of the Storm. The Eye has the power to influence the weather, specifically being able to calm even the most furious storms. When he was first powerful a thousand years ago, the Storm King had already sought to destroy it, and Celestia had given it to the Hippogriffs to keep safe.
Celestia would then task the Mane 6 to visit the Hippogriffs and retrieve the Eye, while the Princesses, Starlight, and Discord would defend Equestria from the Storm King. Discord would be incredulous at first, of course, but he'd soon find out that the Storm King's storm magic is powerful enough to go toe to toe with Discord's chaos magic.
From this point on, the movie would switch between the POVs from the Mane 6 to the Princesses as they continue on their journey. The Storm King and his troops attack Canterlot, and despite their might the Princesses, Starlight and Discord are incapable of being everywhere at once, fighting both the troops and the magical storms at the same time. The Storm King then discovers that there is one more Princess, and orders his general Tempest to find her and bring her back, so he can drain the magic from the Princesses and take over the world (of course!).
The Mane 6, meanwhile, don't have much luck with finding the Hippogriffs, since Mount Aris appears to be deserted. While still there, the group is discovered and captured by Celano's pirates, who are working for the Storm King. After convincing the pirates to rebel against their overlord, they ask where the Hippogriffs have gone, and Celano tells them that the only thing she knows is that when the weather began to turn and the Storm King's return was imminent, the Hippogriffs just disappeared. She jokingly suggests they might have fled under water, where the Storm King wouldn't be able to find them. Twilight thinks that Celano could be right, though, reasoning that the magic of the Eye could probably be tapped to do other things than simply calming storms.
Before they can put this plan into action, they would be discovered by Tempest (in the same way as before, through Rainbow Dash's Sonic Rainboom), who attacks the pirate ship with her own airship. They escape by hiding themselves in a storm cloud, an effort coordinated by Rainbow's skill at weather manipulation and Twilight's magic, but once they've escaped Twilight is frantic that Tempest's presence here must mean that Canterlot has fallen and that everything is up to her now as Equestria's sole remaining Princess. Her friends remind her that she isn't alone, but Twilight doesn't seem to really hear it.
The pirates drop the Mane 6 off at Mount Aris, and Twilight uses her magic to allow them to breathe underwater while they look for the Hippogriffs. The scene in Seaquestria would then play out much like in the current movie, with the added caveat of Novo explaining that they indeed used the Eye to transform themselves into sea ponies in order to escape from the Storm King, by exploiting the nature of its protective magic. Novo is reluctant to hand over the Eye, feeling the protection of her own people is her most important mission, as well as believing the risk of delivering the one thing that might stop the Storm King directly into his hands is just too great. Twilight is unable to convince her, tells Pinkie and the others to go have fun with the sea ponies, and attempts to steal the Eye. The subsequent argument on the beach does lead to Twilight getting captured, just like in the original movie.
Tempest takes Twilight to Canterlot, where the Storm King coldly dismisses her instead of restoring her horn like he'd promised, and Tempest begins to realize that Twilight's pleas for her to turn away from the Storm King might have been genuine. At the same time, the other ponies and Celano attempt to sneak into Canterlot to free Twilight, but are captured and brought to the Storm King.
At this point, the Storm King has all but won, and he finally begins the ritual to drain the Princesses of their magic in order to bolster his own (Starlight and Discord are locked up in cages made from the same material as the Changeling hive to prevent them from escaping, but the Storm King has no interest in Starlight's magic because it is just that of a unicorn, and he simply doesn't know how to drain Discord's magic so he decides not to bother). Tempest, however, turns against him and frees Twilight and everyone else. The Storm King, enraged, decides that he'll simply level all of Canterlot with a storm while his troops battle with the ponies.
Then, in a Big Damn Heroes moment, Novo and the Hippogriffs show up with the Eye, and they use it to calm the Storm King's storms and nullify his power. Unwilling to be beaten, he charges Novo and manages to wrest the Eye away from her, but in doing so he sends himself tumbling off the balcony. He tries to use the Eye's magic to save himself, but in his haste (he is falling to his doom, after all) he messes up and instead of giving himself the fortitude to survive the fall, he turns into a statue and smashes into pieces on the ground below, along with the Eye.
In the epilogue, it's shown that fragments of the Eye still retain enough power to enable the Hippogriffs to switch between their normal and sea pony forms, and each of them is given a shard to wear around their necks to make switching easy, allowing them to choose to live on land or under water. Meanwhile, Tempest is forgiven for the things she did in service of the Storm King, and Twilight is forgiven for nearly starting a massive international incident by trying to steal the Eye. Both learn a valuable lesson about friendship somewhere in all of this.
Maybe I'll write this as a full fanfic someday.