The problems comes in when you take into account the pilot doesn't always know whats best for him.
I know that a pretty arrogant and even silly thing to say, but 99% of the time the PIC is simply concentrating on getting his aeroplane from poin a to point B as quickly as possible with the least ammount of fuss.
The ATC is generally worried about getting half a dozen pilots from point a to point b as safly as possible, while accomodating the Maintenance crew viechiles working on the surfaces, the technicians testing and fixing radios, radars, telephones, contractors working in the tower, military requirements, legal requirements, procedural requirements, and stilll keeping his lisence.
Yes you could have probably made the departure quire happily from the intersection, but it probably fitted the ATC's plan to have you go full length. Maybe he needed the extra 30 seconds for a vehicle to vacate the runway, or for the ILS calibration aircraft to finish a run, or to see if his radio can be read 5/5 all over. Or maybe it was a wake turbulance/vortex seperation.
Safe Orderly Expeditious. I hate to spout the "party" line, but we have to take everything into account. While getting your C172 from here to there is your number one priority, you could well be our number 26th priority.
Especially when we've got to take into consideration things like faster jet traffic wanting to depart behind if you are on an SID, we'd prefer you to be delayed one minute burning the small ammount of gas you do than delay a 747 for 5 and burn HIS gas.
We might have zone saturation in the direction you want to fly, so to save having to pass 7 bits of traffic information (14 in total) we sent you 5 miles out of your way.
Generally there is method to our madness. Either ask up if the Freq isn't too busy, or call in after you land and have a chat.
Better still, pop ober to the controll complex for a cup of coffee one day as ask the people face to face.
27F