I think any system of ranking teams must take care to focus as much as possible on the ones that are relevant and fair. Let me define a few terms. Of course, the results themselves are also relevant, but so are things like game location. Independents have more control of their schedules than teams in conferences, but they have a limited number of opponents who can play on a given week. I'm not suggesting we ignore conference schedules.
Teams do control to some degree their choice of conference.
A rating system is a method for evaluating teams that is not based on opinions beyond those of its creator. The BCS is more of a poll than a rating system, but it's really a little of both. With all that said, let's examine what data is available and how relevant and fair it is. More so with non-conference games, but fair either way. Score Obviously both relevant and fair.