Here is one tip for NMM:

If a mod asks to replace a file that is NOT from another mod, do NOT let it replace it on the filesystem, because you cannot roll back.

I installed Enhanced Character Edit for some textures that required it. The mod asked to replace chargen.dll and a few more files in the SKSE and other folders. Since then CTD as soon as SKSE is loaded with some error GetUseSound function doesn't work.

After ~2 hours of troubleshooting yesterday, I am going to reinstall Skyrim

I heard Mod Organizer (MO) is good in patching and version handling (like a repository, which is also generated from several different sources and patched versions), but I like having manual access to some files and it is known to cause issues with certain mods.

I watched the Gopher videos, but do not want to hop onto a hype here.

I do run a few SkyProccer like ASIS and Automatic Variants and combined with SUM.

I like to bring all images to one resolution and compress them with Optimizer in loose files form and BSA archives.

These two operation would each produce one override patch or do I get an override patch for every single mod or file that is changed?

I would like to do some ini tweaking in the Data/SKSE/Plugins folder, which I believe is also handled by MO and I would even for small ini changes need to run i.e. notepad++ from MO then.

It works OK with NMM, but then you are stupid or do not pay enough attention, like I did yesterday and *bang* Skyrim is broken.

Anything above that does absolute not work with MO?

p.s. one addition:

For the override with optimized images, it would mean I have one gigantic override patch at the end of the list for nearly every single image in the official, DL and mod content?

That's not true, if I understand you correctly (i.e. that you mean "another mod installed by NMM"). If I install a replacer with NMM and it overwrites something, it WILL restore it on uninstall. I've checked this several times as I'm using both NMM and Wrye Bash - and sometimes install simple replacers manually as well.

I use RCRN with external installer for example, it puts its shaders.esp and textures into the Data folder which NMM doesn't know about (another mod which might cause trouble with MO). Most of the files obviously have mods installed via NMM and changes are tracked, those can be rolled back.

No idea where the other files came from originally that were replaced and I cannot remember all their names, which is my own fault. But I strongly believe, this caused the issue that after I uninstalled the Enhanced Editor the game would crash. Now that I think about it, I could just reinstall it but the faces look weird, especially the cheekbones.

It could be anything from Auto-Recharge wepons over Footprints or whatnot, too many mods with scripts

p.s. another theory. It might be MO is more stable because it restricts users to install mods in one predefined way and give them no direct access to tune or break anything (literally everything is menu driven)? The decision would be flexibility or stability.