Well the truth for pretty much all these answers is "I don't know", but lemme take a crack at each of these... I personally believe the story is going to continue to build up to a 3-way war between a group that Osbourne rallies, The Rebels, and King Genesect's army, with the mysterious unknown leader of the Dragon Nation being the leader of The Rebels...
I believe the war will be the major focus of the next season, where members of the competition will be partaking in a group Osbourne (potentially with the help of Nero) rallies together to fight the two major enemies of The Rebels and King Genesect's army, with a lot of potential for bringing back previous characters and using different locations for parts of the war. As for who will win....most likely Osbourne's team would win, but I could also see a surprise twist where King Genesect wins and then later on you have an arc involving overthrowing King Genesect's tyrant ways and restoring the nations to how they once were.
I believe that in the end, Ivan will continue to push for Isolation, until some point later (potentially next season) he will see the error of his ways and support Osbourne in the war, potentially helping change the tide of a major fight.
I can easily see the pirates tying in as a big portion of the Rebel Army, perhaps with Gilligan even being a major role in the Rebel's higher-ups.
Really, anything could've happened to them, but I think that they were captured with intent to be persuaded to join the Rebels, with Hunter being convinced that the Rebels were the weakest team and that the Governments would surely stop them without his help, and Arcedula being bribed with it's item.