It would depend on how the imagined manual trans would shift. I mean, I enjoy driving most vehicles with manual trans but there are some that I'd rather have the auto. I don't like how the 6-speed feels in the super duty powerstroke so I'd take the auto, granted I know there is no longer manual option. In the ram with the cummins, I prefer the manual, especially on the older 5.9 with the NV 4500 or 5600 trans.
I don't mind the auto in my EB though. I seems to have the right gear everytime and if nothing else there's always select shift.