Dabner: I don't think there is any difference between GOTY and vanilla on gog ( except the DLCs of course )
So probably your imagination, or just your pc specs being older I guess
It could be a lot of things but I'm pretty sure it's not related to the GOTY

yoginc: I guess it's my imagination then. But it's definitely not that my pc specs are older though as this was purchased just last year and the components are pretty recent and obviously exceed the recommended requirements.

yoginc: I used to play the vanilla witcher 3 with separate addon DLCs about a year ago and it used to run excellent on my system with 90+ fps at all maxed out settings.
My windows crashed sometime after that and had to reinstall both it and gog galaxy 2. However, when installing witcher 3, I noticed I now had the goty edition of the game which I later realised is separate from three vanilla+DLC (my saves were lost too.)
Now, I'm starting to notice the goty game's performance is not exactly the same it was when I played the original. I can still play everything on max with the same high framerate but the graphics look kinda bad in a subtle way and not as crisp as what I experienced in the original. Also, I experience some micro stuttering which although not frequent kinda bugs me. Or is this all my imagination?

My system specs for reference sake:

Windows 10 build 2004
Intel core i7-9750H
16 GB DDR4 RAM 2666 MHz
Nvidia GTX 1660 Ti (driver 451.67)
Game installed on 2.5" SSD (WD)