There are other big picture costs to consider too.
RPT operations need to be able to publish a schedule and keep to it. If you then want to vary cost index on each flight depending on the vagaries of fuel prices you will surely incur other costs not considered by the CI concept.
Say the cost of fuel rises significantly over a short period of time and you therefore decide to use a lower cost index. You would have to ask some questions first...
How much does it cost to arrive later than the published schedule?
Would this not put pressure on passenger connections, aerobridge utilisation, ground staff resoucses, as well as on-time departure for the next service?
How much is THAT going to cost?
It's a can of worms!