Basically I agree, it can be a problem in complex class hierarchies. However:

• We now have the lovely NEXT that allows us to write AUTOLOAD routines that gracefully decline. I would imagine that it will even be efficient once perl6 hits the streets :-)
• I don't have an issue with AUTOLOAD as long as the module author documents it's presence.
• It's nearly always possible to get around the problem with a bit of trivial object delegation.
• If your code isn't OO it's not an issue