I don't see how Capacity points are so complicated Yoshi! I mean, they are generated pretty much automatically via standard player actions (building RR's, improving tech level of rail system (industrial/commercial techs), building relevent improvements and increasing the physical size of your cities (thus to some extent promoting quality over quantity of cities)). It could be as simple as 1 RR connection=0.4CP's in the early industrial age, with the value increasing to 0.6CPs, 0.8CPs, 1CP etc with each subsequent tech boost. Improvements and Small Wonders could be a flat 25% boost to existing Capacity Points. Then, each Capacity point might increase your per turn income by 5% of current rates (so, for instance, a nation which earns 300 gpt might get +15gpt for every free capacity point). Of course, these numbers are just arbitrary, and would rely on game balance.
The benefit of the CP system is that it not only solves the MILITARY anomolies of the Civ RR system, it also helps to solve the ECONOMIC anomolies-as it would replace the rather ridiculous +1 'gold' per RR tile in your city radius system. Instead, the number of PHYSICAL connections your RR's make AND the size of the cities it connects to, will determine the amount of extra income your rail system generates-balanced against its costs.
Of course, the key issue is that, whilst CP's are generated per connection, cost of the infrastructure is based on a per tile (or per x tiles), meaning that empires which cover more territory and/or have smaller cities, will have to pay more for the RRs they need in order to generate their capacity. At the same time, more prosperous nations will have much more to lose in land wars, as the 'cost' of moving units could become prohibitive!
Yours,
Aussie_Lurker.