>>23321264World was the first one to have everything all mixed up. So you'll do a level based on 0079 that later has SEED characters show up, or a level based on Zeta where you need to back Domon up later.
Genesis takes it back to levels following series events, but ties character unlocks to quest completion, and made the mid-level events that spawn reinforcements no longer optional.
Cross Rays adds in raid groups, so you can have groups operate with no warship, dispatch missions where you send a group on a mission and get rewards when the time elapses, and otherwise improves QoL quite a bit across the board.