The -200 had no A/T and VNAV so the -300/500 were operated without either as were the -700. Southwest also pushed Boeing to design the "classic" configuration of the display units (resembling the non-glass configuration of the -300/500 they operated). Thankfully Boeing made this a customer option.
Some other operators also made use of this, such as Continental/United until the classics were retired (simple software pin change to switch to the regular display set up).
And yes ManaAdaSystem, Boeing could indeed force the change, and Southwest could do little about it. Ultimately they value the customers longstanding loyalty, and to the extent that Southwest gets a full tank of gas on all their -700/800 deliveries out of KBFI, to this day.
I'm sure ure most other big NG operators dont want any major changes either. Pilots excluded of course