Interesting observations.
It would appear that Virgin, Central and TransPennine are generally getting it right but Northern Trains are failing miserably by either providing too little capacity or far too much.
The other TOC's seem to have trains that are better suited to the services they provide.
I assume that the class 323 operated local services on the Crewe-Manchester line are lightly loaded because the affluent residents of Wilmslow and Alderley Edge prefer to travel into the city in their posh motors.