Thoughts to consider.....
1. LRC and CI values have no direct relationship and many LRC values in QRH's are poorly or not corrected for wind.
2. The most accurate CI values are very airline and city pair specific.
3. The FMS is an enabling tool for the autopilot to fly CI profiles and its predictive and analytical capabilities are limited by the data entered.
4. Modern flight planning systems are far more capable of accurate analysis of flight profiles than an FMS.
5. When comparing the Fuel/Time for a different CI while in cruise using the FMS you are only doing a comparison of the remaining flight time and phases and are not comparing the total time/fuel changes. This is a fundamentally flawed comparison methodology.
FMS's are wonderful tools, but like any tool the understanding of its limitations and when and how it should be used is critical.
Lastly, the Airbus "Getting to Grips With Cost Index" publication has lots of good information, but it is outdated because all the assumptions are based on much lower fuel prices. The information contained in it must be tempered with that in mind.