Part orientation mismatch

[Philippe Hurbain]

If I am working with a Technic Brick I would expect a pin or an axle to be placed in the same direction as the holes in that beam. 
If I am working with an axle, I'd expect a bush to be in the same direction as the axle.

For some strange reason that eludes me they normally are not. How can I change this behaviour?

Unfortunately no (*). Many parts have orientation set a long time ago in a not so clever way... Since they are official, changing the parts is impossible (that would break all existing models in the field!). When we encounter a part whose origin/orientation is really, really bad, we correct this as a variant of the part, and make the old version "obsolete". It does no longer appear in sorted parts so it should be not used anymore, but its code still exists so old models using it are not broken. But this remains an exceptionnal procedure as it clobbers library and creates "pseudo variants" that complicate inventories.

(*) Maybe a clever software (hint, hint, LDCad...) could receive a new meta in its shadow library, changing default initial orientation and origin of those parts. I think this matters mainly for technic parts, but I agree that having default orientation of pins ready to be plugged in Technic bricks, beam holes in the same direction as those of Technic bricks, bushes and gears aligned with axles and tow ball pins origin in the middle of ball... yes, that would make life MUCH easier