Matruchus: The patches are not a gog problem at the moment though. The devs haven't yet updated the gog version since ingame updater can't find any new patches either.
Vorastra: They have updated the GOG version. A friend of mine tried a few days ago and the in-game updater currently offers the 2.0.0 update. If it is not working for you then I'm not sure why.
As xxSunSlayerxx already said. There has already been a new update to version 2.0.1 since version 2.0.0. update broke a few things and they had to be patched and a few new features were added. The patch is not yet available for gog players making multiplayer incompatible with other online players.
This is the
content of new v 2.0.1 patch from 29th April:
The First
Added Lab building: consumes ore and generates research.
Scalable resources now automatically start at Level 2.
Added Infuser building: consumes a lot of base materials in exchange for upping the level of a scalable resource.
Fixed buildings continuing to be built after moving the Replicator away.
With a Replicator selected, you can now order it to move to a planet and immediately queue construction of a Core/Transmuter/Strip Miner.
Misc
Fixed an issue that caused crashes on older Intel HD cards. Intel cards are still not officially supported by the game as a whole.
Added "Engage in System" and "Hold Fire" to the engagement behavior menu.
Added "Raiding Range" to engagement range menu. The flagship will try to engage at the maximum distance that its supports can raid at.
Fixed being unable to de-queue certain technologies that only had Study unlocks.
Heralds AI recieves fewer refugee ships when playing on Normal or Easy difficulty, to match the penalties to expansion rate other races' AI get at lower difficulties.
Fixed Nano Mesh and Liquid Armor interaction causing continuous damage to the ship.
Carrier ships with no weapons of their own now have an "Attack" command to let them direct their support ships for raiding.
Fixed Annex System votes permanently marking a system as contested, disabling abandoning planets or removing buildings.
Fixed newly spawned Beacons not marking their system as always safe for jumpdrives to jump to.
Fixed Miner default design not appearing for certain races.
Fixed Beacon Armor ore cost scaling off the wrong upgrade.
Mono cost to build population now goes up if you gain empire population and down if you lose it. (eg through capturing/losing planets)