We (a red coloured Australian carrier) operate NG 737's and use a CI that is airframe and route specific.
The aircraft are from different leasing companies, which means different maintenance costs, and we have a number of different engine/airframe/winglet configurations.
We cruise quite slowly, often below 20 when our competitor is cruising at around 120.
The CI is shown on the flight plan and our SOP is to fly as close to optimum/flight planned level all things considered. If you load extra fuel/pax/freight of course you may not be able to make the planned level, in which case you adjust accordingly.
We also have a published list of CI's and also routes where tankering is to be considered, subject to the usual considerations.
I personally don't believe that this removes the ability for a captain to cruise as required to achieve the objective - ie he/she can cruise faster/slower/lower if necessary - as long as they have a sound operational reason.