There are many types of brakes, all designed for the same brake levers (i.e same amount of brake cable pull) so the braking force you get out wont vary vastly I guess [I am talking as an engineering student and not a bike mechanic].
I suspect the brake pad and cable will probably play a big part here. If the brake pad is not very good, then you'll probably be pulling on your brakes a lot harder on average. The harder you pull your brakes, the more the brake cable stretches (each time you brake, not in the long term - the steel cable does, in fact, behave like a very stiff spring!).... and so more of your hard work in pulling the brakes is wasted, stretching your brake cable.
I would definitely swap for koolstops anyway (they are longer pads that feel a bit softer so I'd hope they'd be better for my rim too), their braking performance is better than my stock pads anyway.
Brake cables are quite a substantial factor for rear brakes because the cable is very long - the longer the cable, the less force required to stretch it by a set amount.
Maybe someone on here can recommend good, stiff brake cables?
Anton