Jun'ko is currently a Rear Admiral in the LSF and is teaching at West Point.
Trent? Look: Trent is a superhero who could hold off entire fleets, win battles when outnumbered 6 to 1, bring down a Nomad battleship in a heavy fighter, be the first human to survive a face to face encounter with a Nomad (and dive into Hakkera's cargo hold without just missing the ship and falling down that shaft...), dual-wield pistols and actually manage to hit something with them, and other such feats. Putting Trent anywhere -near- the game is gonna unbalance it. =P. Though I'd assume he's doing precisely what he was asked to do 16 years ago - he's the Order's eyes and ears (and epic superhero) in Liberty, no?