Introduction: I've been thinking about the roles the Cutie Mark Crusaders will play in the Shadow Wars Storyverse. Here are the results of my speculations, some of which I've obviously had in mind since I started Twelfth Equestriad Interview.
Scootaloo's destined for glory in battle, which is not always the happiest destiny, as Luna could tell her. It means that she's going to fight a lot, and live to tell about it, and it's very likely that many of her battle-comrades, among whom she will have made dear friends and possibly even found lovers, will fall around her, leaving her to wonder why she was spared. The real reason, of course, are her quick wit, her excellent combat reflexes and her special flightfield (which will let her execute defensive maneuvers impossible for most pilots). But she's going to see the wars end with the final victory in 1524, a field officer with the Aerospace Guard at 34, emotionally-burned out, loaded with survivor's guilt and utterly unsure how to handle the sudden peace.
She turns to keeping the peace as a general officer of the Aerospace Guard in the 1530's and beyond. After having lost more than one beloved during the War, and becoming certain that happiness is impossible for her, she finds love afterward, marries and winds up fulfilled in both her professional and personal lives. She has several children, some of whom follow her into the Service, carrying on the military traditions of the Fleetwings and Feathers, the families of her long-dead parents.
Sweetie Belle has a less combative destiny, though it's also tied to the war. As she grows to marehood, her great singing Talent develops. Glittershell, who also wants to be an entertainer, is increasingly her best friend in their adolescence, and both of them become good friends of the Great and Powerful Trixie, who brings them to the attention of her (eventual) husband, the theatrical promoter Piercing Gaze. With Piercing's promotion, their singing career takes off -- they do duets, with Sweetie singing soprano to mezzo-soprano (she has a wide range) and Glittershell contralto. In their twenties and thirties, they entertain the troops in the War and afterward are iconic voices of their generation.
She is forever haunted by her memories of the many friends she made among the troops, good Ponies who loved her and went off to die in battle. Future generations of the Guards sense this, and even as she ages, she remains their darling. She marries once, but it ends in divorce; a child results.
Apple Bloom has the longest-term influence on the future of Equestrian civilization of any of the Cutie Mark Crusaders, for she becomes an engineer, scientist and interplanetary pioneer. Her talent is to encourage growth through chemical engineering; she studies alchemy, botany, biochemistry, chemistry and engineering, graduating from Manehattan's Gather College in 1511 and the Morgan Institute of Technology in 1516, doing graduate work in the field during the Great Changeling War. She marries in 1518, but decides to delay having foals until the end of the War.
In 1524, she's the life support chief officer on a transport on which her husband is chief engineer, heading for the Moon to establish an outpost there against possible Shadow infiltration through the Lunar portals. Enemy fire destroys the bridge and damages the powerplants; she has to flush the main sunfire reactor to avoid the destruction of the ship. The engineering crew was trapped in there, and so she basically has to kill them -- including her husband -- to save the ship. She then manages to repair the auxiliary controls and crash-land on the Moon.
She establishes the outpost, and cannibalizes the transport in the process, using the additional resources to set up not merely a small outpost but a self-sustaining colony. This colony becomes the nucleus of the Equestrian Lunar colonization of the ensuing decade. Apple Bloom bears the child of her dead husband on the Moon -- the first foal to be born there -- and leads the colonization first of the Moon and then of other worlds. She eventually remarries, and becomes the matriarch of a large family -- the junior branch of the Sweet Apple Acres Apples, the one not led by an Alicorn Princess.
Conclusion: The Cutie Mark Crusaders have bright and special futures -- which is one reason why their Cutie Marks took so long to come in.