The biggest debates around watch order I've seen in recent times is with the main Fate series and Monogatari. I watched Monogatari in release order and honestly the big debate is around the placement of kizumonogatari. Do you watch it at the beginning or really late in the series. Although I have seen some dumb orders which basically take out episodes out of one season and insert them into other seasons to make it look chronological, it was the stupidest thing ever and it was a bunch of sheep who wanted to follow Nision's order.
As for Fate the entire problem is that the Fate route apparently doesn't have a good adaptation. Granted, I have only watched Fate/Zero so I wouldn't know. If I had to pick one I'd choose release order for everything.