They all have flaws...just the AP poll's biggest flaw happens to be UNI and even more WSU. Kansas is a legit two seed but having them #1 all year shows a flaw in the RPI.
I think the Sagarin ELO portion is actually the best individual metric tool for selecting teams based purely on who they beat resume comparison type thing. We're 11, UNI is 23, WSU is 16, KU is 8...it's the easiest ranking to easily point to who beat who and accept it all. Great potential tournament selection tool. Not perfect but simple, transparent, and defendable.
BPI has its own messes too, BPI has thought Ohio State was awesome most of the year.