Unfortunately NMM was constructed using Oblivion Mod Manager code. It was already outdated by the time Fallout 3 was released.
NMM was also worked on by many people that worked on it a bit and then left the project, then new people came in and took it over and then left again. It's coding is a mess.
It was impossible to fix without starting from scratch, which was what Nexus did. They Started Vortex from scratch because they couldn't fix NMM, due to how outdated it is.
Some things NMM will have problems with (from the top of my head):
- Installing large mods (will sometimes not get all the mod files).
- Installing scripted "heavy" mods (might not get all the scripts in the game properly).
- Sometimes (and luckily this seems to be very rare) will delete all your mods.
- Unpacking fomods, specially large ones (same problem as before, will not get all the mod files)
- Memory leaks can occur.
- NMM will mess up other mod managers you might be using (for example, let's say I am using FOMM for Fallout New Vegas and NMM for Skyrim. It might mess up your FNV FOMM even though it is not the FNV mod manager).
- Might not remove all the files from mods when uninstalling them.
- It installs into you Data folder just like FOMM does. This is not good practice since it can break your game when a mod is not properly installed, or NMM failed to install the mod correctly. It might leave remains of mods after you uninstall them and mess up your game. Mod Organizer, Mod Organizer 2 and even Vortex do not touch your Data folder, meaning your mods will not mess up your base install of the game.
- It will overwrite files from mods if they conflict (while MO, MO2 and maybe Vortex will not)
- Might have problems with NVSE plugins.
- Might have problems installing mods dependent on DLC.
- There are more stuff, but I just woke up and so my memory doesn't work properly.
I just found the Nexus announcement about stopping development of NMM. It has a history of NMM and it's origins. While keeping it civil and not calling NMM any names, it's still pretty self explanatory:
https://www.nexusmods.com/news/12905