I'm a smaller shop, and the print floor is pretty cramped. Even so, I could never see ditching the manual.
I have a Hopkins 6/4 that you'd have to shoot me to get. I still use it every week, some weeks every day. Oversized prints go on the manual, because I don't have currently another option. And with sleeves, weird placement jobs, low piece count....I usually pick the manual.
Hoodies with large white blocks of color--ESPECIALLY low quantities--that works better on the manual for me. By the time I get all the platens warmed up, different adhesive, ink all warm and happy....I just can't see setting up the auto for those little jobs at this point in my development. Your shop may be different.
But my auto is slow to setup (for me anyway) than the manual which is fast to setup and breakdown. I tape my squeegees for the manual. (SO FAST!) If I had a better way to clean winged floods and squeegees, and a pre-registration system that really worked, I might have a little different story.