First, not "every" Focus makes noise when shifting. I've driven several and none had that problem. Second, you don't say how many miles your Focus has, but they do get better with age.
Noises and other transmission weirdness seem to have two main causes: out-of-date software (has your car received FSA 12b37?) or an internal oil leak that contaminates the clutch plates. The software issue is easily addressed by your dealer. The clutch issue may be a struggle if there isn't a visible fluid leak.
Try it again with the dealer. See if you can take a mechanic on a drive with your car and then one off the lot. Or see if a mechanic will take your car home overnight. Be as specific as possible about the behavior you're experiencing and when it occurs. Look over this board for some success stories dealing with oil-contaminated clutches, print and give to the technician. If this doesn't work, look for Crystal or one of the Fords reps that monitor this board: they can get extra attention from the dealer network.
I don't think the difficulty getting things fixed is because Ford is trying to avoid the issue. The real problem seems to be a dealer network unprepared to deal with a new technology.