Some differences between the ratings I produce and those Wilson produces: beating a bad team will never hurt you with my ratings, as they will (slightly) with Wilson's; an undefeated team, in Wilson's ratings, will find its rating based heavily on that of the best team it played, while mine may be less impressed if you play a single good team and more if there are three or four comparable near-best teams; big upsets are more attenuated in my system (losing to a really bad team will, broadly speaking, only hurt you twice as much as losing to a team of about your calibre, where in Wilson's ratings it can swamp the rest of your season). And so on.
There should follow a general discourse on the fact that, using no score information, there's only so much one can say about an undefeated team; indeed there might should follow a general rant about the BCS thus handicapping its computers in the very sector of their ratings that has been given the greatest importance, viz. the top of the ratings. Of course, such rant should also probably be mitigated by the observation that the purpose is to win games, not roll up large margins, and perhaps the rant should be directed at atheletic directors who construct weak schedules. Even that point, though, falls to the fact that Utah's schedule, for example, was put together at a time that Air Force and BYU could have been expected to be better than they were, Texas A&M and North Carolina were not fluff teams, and nobody at Utah could really have been expected to foresee that their team would go through that entire schedule and a BCS bowl game without winning by less than two touchdowns. It's a real shame they didn't get a better opponent for the bowl game, to tell us how good they were.