One thing to consider, which may or may not help simplification, is the intersection of fares, peak/off peak, and user demographics. For example, seniors and people with disabilities are often in different fare classes. Some college students have bus passes for some of the local agencies, but not all. Primary and secondary students might have free rides during busing hours, but not during other times, etc. Therefore, looking at fares from an multidimensional array perspective, rather than a flat list, might help.
The most comprehensive study on the requirements for a fares protocol that I am aware of was undertaken in the UK (where we have particularly complex fares systems because they are essentially commercially determined by each operator).
See http://www.dft.gov.uk/transxchange/farexchange/index.htm
This work has been an input to the Eiuropean work currently under way to define a Fares Exchange protocol within NeTEx. This is on-going work - and I will need to find out what, if anything, is available to describe what is envisaged within that emerging European Standard.
What both pieces of work confirm is that a universal protocol for the handling of fares is far from trivial. And whilst the UK work tried to cover all approaches to fares structures worldwide, I suspect that there are some local variations that may not have been fully covered in the Farexchange work.
Roger
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Just picking up on David's point... does anyone object if, in the interim, the current proposal is accepted in order to enable us to move forward with the definition of distance-based fares for use in the Metro Manila GTFS database we are creating?