My half-awake pondering is that a futuran/commander route goes like. In one ending of a new DLC route, Takumi meets the old woman from SF, and she gives him the ability to actually go back in time with the PLM. All he ends up accomplishing is giving a Day 2 version of himself access to the babyjar, unlocking the route where Takumi spares Murvum and bails with Shion early on. Why does this matter? Because the structure of the game is defensive battles, or put another way, defending Shion (the thing in the Defence Room) from invaders (futurans). Only now it's Takumi and the commanders defending Shion (babyjar) from invaders (brainwashed SDU and human enemies). You can even have Takumi slowly persuading commanders to join as he did with the SDU on route 0. This preserves the game's general structure while going in a completely different direction.