Similar situation for me with both Transport Fever and Transport Fever 2. The issue is save sizes. For large maps, they appear to weigh in at about 73 MB (no mods, though I don't think it's significantly different if you enable any/all of the pre-installed mods). This appears to be consistent between both games. Three saves at that size and you've more than filled the 200 MB per game limit.

To note, I do have a campaign save for the first game that is only 24 MB. I'm pretty sure the size difference comes down to the smaller map size. Transport Fever 2 is currently unplayable for me (immediate crash to Desktop on starting any new game/loading saved games), so I can't test the campaign save sizes for Transport Fever 2.

I don't think there's anything we can do about the save sizes, aside from playing on smaller maps, but you can adjust the autosave frequency and retention to reduce the number of autosaves you end up with. That can only be done from Settings in the main menu. You can then delete unneeded saves from the Load menu (on which the Delete button is on the right).

I do not use the Cloud Save System and it runs fine ( use only my desktop for Transport Fever 2 ).

But I have seen that people have problems with CloudSaveGames in the Steam Forums too. So I think that because of the huge savegame files neither Steam or GoG Cloud Savegames work.

You can try to reduce the Autosave Games from 10 to 3 ( I use 5 ), in the options ( Main Menu ). Maybe GoG CloudSaves will work. Think I read that Steam CloudSavegames get problems when they are bigger than 140MB.