Thanks for the answer.
Cheers,

I am not an expert but it looks like it should be with some tinkering.
https://skse.silverlock.org/

Try it if you like and don't forget to manually move you profile files to the app/local folder each time you add a new mod.

I had to install SKSE manually in order for it to work. When I instead tried to install it automatically with the Vortex mod manager, then it kept giving me an error message and would never work.

Forget about the name as that will only confuse you, just look at the game version.

On GOG, AE/SE (they are exactly the same) it's 1.6.659, and look for that on https://skse.silverlock.org:
Current GOG Anniversary Edition build 2.2.2 (game version 1.6.659)

I've heard that there's a bug in the first SKSE release for 1.6.659 that prevents certain SKSE plugins (Engine Fixes SSE comes to mind) from loading, Apparently, there a new version to come out in the next days. Not sure if that's really true, though. But while I can totally run SKSE on 1.6.659, several plugins that *should* be compatible simply won't load (SKSE/Trampoline.h (186): Failed to handle allocation request).

The new SKSE is out, but unfortunately, a lot of mods (looking at you, SkyUI) still need to be updated for the GOG version.

SkyUI works with the GOG version.
How are you installing it?

I too can't get SkyUI to work properly.

SKSE (skse64_2_02_03_gog.7z) is installed, manually, I can run skse64_loader.exe just fine.
SkyUI_5_2_SE-12604-5-2SE.7z installed, manually by copying both SkyUI_SE BSA and ESP files to /Data folder.

Things changed quite a bit since I've last played Skyrim, seems like the whole paid mods controversy lead to removal of data file selector in the launcher. So I've tried with the latest version of ModOrganizer, it does detect SKSE launcher and also SkyUI (as unmanaged mod), I ticked the required box, clicked Run... and the mod is not loaded. Doesn't seem like the loading order is making any difference.

So next I've tried:
1) either adding sTestFile4=SkyUI_SE.esp to Skyrim.INI and editing sResourceArchiveList2 to include the BSA
2) or adding SkyUI_SE.esp line do the Skyrim.ccc file

Both these methods work and load SkyUI (via SKSE launcher) though number 1 is telling me that mods are now active and achievements will be disabled, while number 2 has no such issues. However In both cases I have a lot of inventory texts starting with $ sign, clearly missing some internal strings (I'm playing with English texts and voices).

I seem to remember all of this "just working" years ago and back then I didn't need to sign up to 3rd party sites for their custom mod installer, a few INI edits was all it took. And now we have... progress I guess. Special Edition. Do I need a doctorate in Skyrimology to install one mod I care about? Or is it just broken on the GOG version?

I found a solution that works for me - it seems ModOrganizer needs an update for GOG version of Skyrim, and said update can only be found on NexusMods. I don't have an account there, nor am I planning to make one - I will not be forced into using 3rd party installers or accounts to play a game from GOG. But the bug report for MO was very enlightening.

In case it's useful to some other (stubborn) people: Install SKSE and SkyUI manually as explained in my previous post. Just copy the files, that's it. You might want to run the original SkyrimSELauncher.exe once to have it detect and set up default GFX settings by the way. You can also set the resolution and borderless mode here rather then editing the INI files. After that stick to skse64_loader.exe (update Galaxy settings as well if you want it to run it instead of the original executable).

Create a text file in "AppData\Local\Skyrim Special Edition GOG" folder (which should exist but will most likely be empty) named plugins.txt, and then put one line into it:

*SkyUI_SE.esp

And that's it. SkyUI will now load and work but you will get the annoying prompt about mods and disabled achievements. To get rid of that also modify Skyrim.ccc file in the game installation folder, add

SkyUI_SE.esp

at the end (note, no asterisk here). This will confuse Skyrim and cause the mod to be detected as Creation Club one - but that alone is not enough, you need the plugins file too or the strings will be broken for some reason. This combo seems to work just fine though.

There is a new version of SKSE - 2.2.3 but is appears to be the source of quite significant stutter in my case, where SKSE 2.2.2 works fine. So beware.

2.2.3 does not introduce any stutter to my game, but I don't run many mods. Try finding another culprit

I think you are right. I've tested some more and I have the same problem on 2.2.2.
I believe the problem may be caused by another mod (FNIS) or a combination of the two.
I'll test more later.

Thank you so much !
Being on Linux with Lutris, I try to install SkyUI manually since a week but without success.
Your solution works perfectly ! Thanks again.

I don't understand the comment. How do you want to download mods and other things for Skyrim if all mods are only on NexusMods? You create an account and download the modifications, so what's the problem if you don't feel like it lol. Many people use Nexus to download mods.

Thank you! This indeed seems to work and is just what I was looking for. It would be even better, of course, if the Data files option in Launcher wasn't broken in the first place... SkyUI is the only mod I want, and running under Wine I certainly don't feel the need to complicate things with some fancy "manager". Simplicity is important. The fewer software components are necessary, the better.