Leeds to London flights don't work as well as Manch to London flights for two reasons (apart from the obvious difference in size between Manchester and Leeds market)
1. The East Coast Main Line works and has worked for years
2. The M1 takes you from Leeds City Centre straight down to Brent Cross.
With Manchester, the West Coast Main Line, although better, is still not there and driving is unthinkable.
Jet2 do offer an early morning flight that is significantly cheaper than Virgin Trains on almost every count. I intend to use it more regularly from now on having just tried it for the first time.