Here's what I'm thinking as far as the epilogue goes, replace the generic old star gazer at the epilogue with a familiar voice. Specifically Shepard's lover, I think if anyone should be telling a story about Shepard, it should be the one who Shepard shared the most intimate moments with.
Have the kid ask questions about everyone else that would help bring closure and maybe even show how the choices you made mattered.
I'm not sure they CAN come up with an explanation as to how Joker and crew ended up next to the Mass Effect relay when it went off, or how he would have time to even pick up members on the ground.
Indoctrination fits a sufficient amount of the game's own narrative, cinematics, and lore to work. Even if it wasn't planned, as Angry Joe said, "Feel free to steal this fanfic."