I also only notice that it's 'choppy' when I look for it. I do notice that it's slower than the usual scrolling. For me it doesn't ruin the game (while I wouldn't mind if it would scroll smooth), so judging the game by its 25 FPS scrolling is a tad superficial in my book.
Choppy scrolling (losing frames) and general 25 FPS Scrolling (cause a permanent motion blur/ghosting) are different things. Sadly Gods suffers from both, and it's still a good game.