Tools to Avoid
Vortex
Vortex was created around the idea of LOOT managing the load order, making modding seem simple and easy (see below why that's a bad idea).While the option to manually order plugins exists, it's designed to be as unintuitive as possible - the user needs to select the position of every plugin from a dropdown menu, based on relative position to other mods (load X after Y, load X before Z), or use a graphical, node based interface.
Additionally, it does not track generated files, and the deployment logic can be confusing to the user.
Vortex also cannot easily export a user's mod asset list for troubleshooting. Users can only export their plugin list as a text file, but not their full mod installation order. This makes it extremely difficult to provide mod lists when asking for help, as the only alternatives are taking screenshots while scrolling through the mod list or publishing collections (which sort mods alphabetically, not in installation order).
Nexus Mod Manager
Outdated/abandoned, have no virtual file system or even dynamic movement of mods with loose files, which can lead to complete mod or game reinstalls in case the user wants to change the load order, or installed mods in a wrong order.
Mod Organizer 1
There is no reason to use Mod Organizer 1 over Mod Organizer 2.
LOOT
LOOT doesn't really have any idea about your mods and their inner structure - it just orders them based on tags in a masterlist managed by volunteers, meaning that it's impossible to account for every single mod and combination of mods.The main issue regarding LOOT in most Bethesda games is that its masterlists are often outdated or incomplete, leading to broken load orders that will cause mods to misbehave. Oblivion is an exception where LOOT tends to work more reliably.
Bashed Patches
These patches have their use cases and in skilled hands can save a tremendous amount of time. It's not that they should be completely avoided period.However, like some of the other aforementioned tools, they are fully automated, and without the oversight of a human being they are liable to misidentify intentional overwrites as "conflicts" that need to be solved. For this reason, it's only recommended to use them if you are both capable and willing to comb over the resulting patch.
LOOT and Bash tags are unused by majority of the Fallout 4 modding community, leading to complete breakage of the automated behavior of these mods.
Mator Smash
Outdated and produces broken patches. The only viable method of automated patching available is through a properly utilized Bashed Patch thanks to its sophisticated tagging system, which allows the user to customize how the generated patch handles individual records.
zEdit/zClean
Neither have any real advantages over FO4Edit and lack some essential features due to their outdated codebase. Support is also limited.
Merge Plugins Standalone/zMerge
Automated merging can potentially cause major breakage in mods, especially heavily-scripted ones.
FallrimTools Cleaning
Cleaning save files with Resaver will only cause issues, there is nothing that needs to be done to save files with a functional setup.
Ordenador/DDSopt
Breaks many textures by needlessly converting/adding/resizing alpha channels, cubemaps and mipmaps. Use BSArch Pro instead.
FO4 Crash Log Auto Scanner And Setup Integrity Checker (CLASSIC)
Overpowered, invasive, and misinformed in many areas. Crash logs require a brain and plenty of knowledge of game mechanics to be read, you cannot simply look at the stack and blame whatever DLL appears the most (even if that worked, you'd still need to figure out the actual cause). In a lot of cases, when the readable info doesn't suffice, you'll also need a disassembler and decoding skills to be able to read the log. For this reason it's additionally dumb to rely on a logger handled by people who can't do RE.