Of course there will be a plot twist. We don't know an awful lot about the story other then that a war has broke out between Osea and Erusea, we still don't know much about Trigger and his actions that led to being part of Spare Squadron.
This could count as a SPOILER but:
My opinion is that there will be a plot twist early on, possibly around mission 4 that leads to Triggers being criminalised. In the mission 6 demo we can hear radio chatter where the other members joke about Trigger having murdered an ex-president. I doubt that Trigger actually did it knowingly or maybe he was framed by the rest of Mage Squadron?
That's just my opinion but I doubt we'll be switching sides, maybe it might play out similarly to AC5 where we become somewhat of an independent/covert squadron to try and stop the war. Considering that AC5 is being bundled with the PS4 pre order, I believe it may play out similar to AC5.