Mod managers are PC software utilities that manage the plugins of your mods in order to get the best experience out of playing with Fallout 4 mods. The best mod manager is Mod Organizer 2 (MO2) because it allows you to create different modding templates for you to launch your game in different ways. This versatility sets it far apart from all other mod managers. The inferior models are Vortex and Nexus Mod Manager (NMM), all available on Nexus Mods website. Keep in mind that MO2 is open-source and not in Beta, whereas NMM and Vortex ARE Beta.
Mod Organizer 2
Mod Organizer 2's unique feature, which sets it apart from all other managers BY MILES, is the ability to create profiles. You can can have 254 plugins worth of mods for each "profile". You could make themed profiles to enjoy playing Fallout in so many different ways possible without suffering the 254 plugin cap that Vortex users experience. Make a Nuclear Winter profile with 254 plugins AND a Zombie apocalypse profile with another 254 plugins. You can make as many profiles as you desire. This function is found at the top of your Mod Organizer menu bar called "Configure profile" . Have fun playing Fallout 30+ different ways!
MO2's strength is that it can help you isolate problematic plugins with its easy to click list of plugins. The plugins do not deploy and they do not shift around. If you are experiencing weirdness in your Fallout game play, such as missing body parts, you can quickly isolate plugins in entire sections, in order to identify the problem plugin. This versatility is not available on Vortex.
MO2 kicks Vortex right in the ass with its ability to highlight and select multiple plugins to enable or disable. This feature is key in narrowing down finding problematic plugins through a process of elimination that cannot be performed in Vortex.
Vortex makes installation and navigation very easy. It does well in sorting, downloading from Nexus Mods, categorizing, display, and linking back to the Nexus page without searching. Its drag and drop platform is its poison water.
Vortex has made installation so easy and accessible with drag and drop that by not thinking about the files you are dropping into load you potentially miss proper installation of UIs an ENBs that require reading their readme.txt for proper installation.
Vortex weakness is its deploy method by creating dummy files and littering them throughout your Fallout 4 installation. In Vortex you have to [install], [enable], and [deploy] each file one at a time.
Mod Organizer 2 will allow you to play multiple Fallout environments (ones that conflict or take too many plugins), ie: FO4-New Vegas, FO4-Arroyo (California/Nevada/Arizona), FO4-Wyoming, FO4-Capital Wasteland, and FO4-London. These environments you cannot play at the same time, but can switch batch back and forth - with EASE - and at will - in MO2! You cannot do that in Vortex. So while we're playing New Vegas and London, you can be stuck fighting a 254 plugin cap at Vortex. Or... you can consider migration.