Saipher604

For anyone still having this issue, since I couldn't find any place where this solution has been posted yet. I've had this problem of long startup times for a long time. The problem seems to be windows defender checking file access or something similar whenever the game launches, the problem gets progressively worse the more loose files e.g. mods you have installed. Adding an exception for the Fallout4.exe and f4se_loader.exe respectively in the antivirus settings fixed it. Alternatively add an exception for the entire fallout 4 folder.

good luck to all!