It's important to distinguish results based rankings from predictive metrics, because they serve different purposes, and therefore can have discrepancies between them.
A team like Air Force is ranked higher in predictive metrics than results-based ones because it has played a fairly tough schedule so far. Conversely, Army has done well against a rather weak schedule to date, so it's results based ranking is higher than predictive metrics. Consequently, you shouldn't be surprised if Air Force ends up dominating them when they play each other this year.
In basketball, Kenpom is the best predictive metric, but it shouldn't be considered in the NCAA tournament selection or seeding process or teams like Clemson and Indiana would've been in the field last year instead of USC and VCU. There's still a strong correlation, to be sure, though. The RPI has its own flaws as far as results-based algorithms go (and it's a rather simple calculation), but so do other algorithms and formulas.