BEagle, I agree with a number of your points but please remember that,as has been pointed out already on this thread, you get cr*p RT all over. Mil, civil, aircrew or ATC, it doesn't tend to make a distinction as far as the standard of rt is concerned.
And the cock-up with the line-up vs take-off instruction was just that, a cock-up, not a problem caused by poor RT. Would it be nice to be able to have a procedure as you suggested as our civ colleagues do-yes! In fact individual units could probably produce a local procedure to do it with station based ac. On a blue-blue day the aircrew would love that kind of flex, but what happens when you have the procedure, it's YLO2 and the spotty oik cocks it up? There isn't much in the way of experienced controllers in towers at the moment!
The point you raised about the CHIRP was spot on though. I remember a number of years ago the stn was having it's post Christmas welcome back flt safety stand-down day and people were talking about filling in paperwork and the stn FSO pointed out the awful record of atcos filing HFORs. One brave atco stood up and pointed out that people previously filing said reports through their SATCOs had been investigated and many had been 'hung like guilty bar stewards' hence the reluctance.
Our OC Ops, very nice chap too-ex Tonka mate don't know where he went, stood up and basically said "chaps if you've been stupid and deserve a roasting then you'll get one. However no-one is going to be hunted down for minor instances and certainly not through filing an HFOR."
Which was all jolly decent because 2 weeks later when I made a god almighty co*k up, we all sat down and had a very adult 'what can we learn from this' session. I think they're trying to instill that kind of a message in the guys from an early stage now, but from what's getting into the "front line" now I wouldn't be too sure. Any ideas Beags?