I didn't get the game yet so I can't test it, nor do I have much experience with Skyrim modding from the time I played it on Steam, but according to the anniversary edition bundle: Do your mods fit/require any of those conditions?

---wrong information---

Going to test in a few min. Will let you know.

The official announcement from 6 hours ago states,
Support for mods requiring Skyrim Script Extender will be added later today.

The Nexus Mods announcement states,
you can expect a GOG-compatible SKSE release in the next few days. That might work just as well, but only Nexus Mods Vortex v1.6.12 and newer is supported.

Seeing as Skyrim is now here, makes for an interesting set of topics.

Regardless, regarding mods so far i haven't used much in the way of mod managers, instead i have a clean installation as a 7z file, then add mods that i expand and play saves from... Though certainly not the preferred way people to use i am sure.

Just redownload everything again from nexus most up-to-date. Something (mod organizer) been updated today, and you probably get older version.

Also, as mentiond above - you instal lat least one outdated mod. SE if for SE, GOG is AE with most important part of it plit to separate DLC as installer and as store item. Looks like GOG version is something between SE-AE.

Also, you better avoid to make thread here in General english discussions. It is general.. .and by community - too much general. If you think you can get answer here faster - you probably right (or not), but probably better then do it in News:Release thread.
Should be someone like you who discuss same issue in Elder_scrolls series sub-forum. Since this is new release - you have for now equal chances to get answer everywhere. later - it is random. For game\series specific forums you at least make it in proper place.

GOG compatible version of the Script Extender is out now according to this page:

http://skse.silverlock.org/

Rule number one is to make sure the versions of the game, SKSE and the mods are correct and are compatible.

I just hope it wouldn't be too much trouble using MO2. Can't stand Vortex.

Just tested it myself using Vortex, everything worked fine... including SKSE.

I can understand why people get confused by the different names and versions. It's very easy to miss that SE and AE today are completely the same game version. AE just has those CCC mods. The older SE version (1.5.97) is from before AE came.

I bought SE now and it's exactly the same version as "AE".

Bethesda's naming scheme in a nutchell...

Thanks all for the feedback. I've never used vortex, since I mainly manage mods manually or with MO2 without issue so I'll try it and see if there's any change. I'm using the same SKSE version that was recommended to work with patch 1.6.whatever the rest is. It's the one labeled for the GOG release, so not really hard to miss. If the issue is just to use Vortex, I'll give it a go and see what happens.

Its not only for bethesda. GOG announe warn that nexusmods need updates come next to GOG release. You need at least one day to wait and not downalod everything any-version you found. Read_me first.

Using Vortex seemed to have solved the problem. I got SkyUI and Random Alternate Start to load properly. Thanks to the folks that mentioned it.

Another option is to manually edit the "Plugins.txt" file.
The file can be found at the following address:
%LocalAppData%\Skyrim Special Edition GOG

Enter this address in Windows Explorer, which will open the local application data folder. Usually:
C:\Users\(your user name)\AppData\Local\Skyrim Special Edition GOG

In "Plugins.txt" must be listed all installed mods with * (astherisc) before the enabled ones.

Example of content:
*My Enabled Mod.esp
*My Other Enabled Mod.esp
*Zombie Voice Remover.esp
My disabled mod.esp
My other disabled mod.esp