I played through the Steam version when the game first came out and the lack of backwards progression in the Steam version is pretty bad. You should be able to play through the whole game again if you want and the GOG version offers that, which is great.

However, on playing through the "Shadow Wars" part, I remember that the Steam version had a very long and drawn out series of sieges for your regions which was widely criticized as grind to push people towards the awful micro-transactions. While I totally agree with the consensus that the micro-transactions were bad and no one should have ever bought any of them, I disagree with the criticism of the length of the Shadow Wars. That extension of the game, holding back only a Kingdom Hearts style final video unlock, really gave opportunity for engaging with the Nemesis system in a deeper way.

When I played through the GOG version, I was expecting more phases to the Shadow Wars so that I'd need to defend my fortresses. I thought I'd need all skills unlocked and my level hitting the level cap to be able to even get to the final video unlock but instead, the later phases appear to have been removed. The game just abruptly ends after you've defended all your regions fortresses one time. (where in the Steam version, all fortresses had to be defended multiple times)

This hurts the game in my opinion. What it really needs is an infinite siege mode that puts constant pressure on your fortresses forever, requiring you to constantly recruit and upgrade more and more captains. In the GOG version (on Brutal difficulty of course) it just seems like it's over too quickly. Maybe Warner Bros listened to the criticism a little too much?

I guess if I really want to play more of the game then I should switch from Brutal to Gravewalker difficulty but still.

I have to post a correction to my original post.
Infinite sieges are present in the GOG version just like in the Steam version.
It isn't a separate mode: you just always have the option of defending against a siege any time by going to where the siege mission is on the map. There's just always one available in every region all the time after you complete the main game.
IMO it might have been a little more fun if the pressure rotated to whatever region was weakest in terms of level so that you had to play them all, but I guess it's OK to let people who really want to just defend the same region over and over.