That was because the DfT wrote into the SE contract the premium pricing of HS1 fares along with a unique RPI+3% formula. Ironically some of this was to try and undo the disastrous anomalies that had been caused by the previous RPI-1% regime when combined with the high weighting of Travelcard fares in the SE fares basket.
RPI+0% is a Conservative Party manifesto commitment and GTR is being run as a management contract on behalf of the DfT. I can categorically tell you there is no chance that Govt will deviate from this in the short term.
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The problem with this and a number of other sensible suggestions is that it is virtually impossible to unpick the current regulatory regime coupled with the manifesto commitment to stick to RPI+0% with no flex allowed.
We have a government that a) wants simpler fares for commuters; b) has removed the ONLY mechanism that allowed any adjustment to made to such fares on a revenue neutral basis (flex) and c) has said there is no money to fund changes to the fares structure. They are pro-having cake and pro-eating cake but there doesn't seem to be any cake.
Not to mention a Mayor of London who has a manifesto commitment to freeze fares within Greater London, despite:
a) no power to do it, as many of the fares within Greater London are at the behest of the TOCs who (I would imagine) would want to be recompensed, given that they took their franchises on the basis of the regulatory increases at the time, and have planned financially based on that.
b) no money to do it- though admittedly that has never stopped any politician before, particularly a Labour one.
So, we have a Conservative government and a Labour mayor who both want the cake and want to eat the cake, but no-one seems to have told the baker. (The BFAWU is probably on strike, admittedly.)