You can go with any route, the story and route are pretty separate. The story is the story its effected by the vault and events like that but routes are more like the flavour (who you will experience the story with). So your free to pick whoever you want as your route partner.
Whatever route you choose has no bearing on who dies after the first bad end. The route is just flavour, pick whoever you want so long as you get the passwords and make good choices its possible to keep everyone alive.
