If you want to be friendly with the Institute and undercover with the Railroad, choose Railroad. If you want to be friendly with the BOS and be mainly with Minutemen, choose Minutemen. I did Minutemen because the Institute is evil (obviously), and the BOS' belief is really flawed, and I would've chosen the Railroad, but it would've caused the BOS to hate me (To progress farther into the Railroad quests you'll be hated by the BOS)