There are at least several variables in providing a good answer to your questions.  For me, the primary purpose for which the lens will be used is the most important variable.  For example, I love doing closeup candid shots of children - not an easy task for a manual focus lens when depth of field is purposely kept shallow, light is low, and one is close to a lively subject (tho small flash is often a good equalizer).  On the other hand an adult or oolder child portrait or landscape situation will usually provide ample time to manually focus and the results are more predictable.

Visual acuity is another important factor for me.  I simply can't see well enough to focus accurately manually unless the light is just right and the object of focus fairly close relative to lens focal length. Short primes can be particularly difficult.

I have one of the new Nikon AF-S 50mm f1.4s. It auto focuses fairly quickly and accurately even at f1.4, but it can't match manual focus results of my old Nikon 55mm f2.8.  Some of my AF candid shots have not been as sharp as I would like, but without AF I would have missed not only these but many shots that were sharp.

Bottom line is you'll have to continue to do as you have and make up your own mind and live with the consequences.  I resigned myself to that fate long ago.

I can swear there ain't no heaven but I pray there ain't no hell. _ Blood Sweat & Tears