In the previous versions of Automation there was more car bodies than in the latest version. Those bodies were from following cars: Škoda Felicia, Peugeot 306, Toyota Hiace, etc. However, today I noticed that these bodies are missing. Why were they removed? And is there a way to return these bodies to the game?
No, they aren't, i.e. I haven't found them on Steam Workshop. They're listed in official cars for Automation on IGCD.net.
Automation recently switched game engines, so the Campaign and some body styles aren't in the main game yet, although I believe you can still launch the game in the old engine and play the campaign.
New version of automation don't have them all ported yet, I don't know if they are going to port them all or if they are going to make new ones instead or make new ones and port old ones, but yeah, there are few body styles in old version that I miss in new one. For example one that was bit like Beetle.
