I'm going to assume your talking about rangers. Yes the M5OD trans does have issues with the slave cylinders, although I've had no troubles from mine in 185K miles. The shift rail plugs tend to leak on the M5OD, which if not watched, can lead to trans failure. Despite these issues, I'd take a M5OD ANY DAY over an automatic, especially the A4LD. It's geneally regarded that the A4LD is the weakpoint of any ranger. Just look around the site or google for more input on the weakness of the A4LD. In terms of reliability, go with a stick shift.
In personal preference, I like a stick shift. They are simple, easy to maintain, more efficient, and more fun to drive. Also, I'd rather change a clutch than an entire tranny.