Two concerns off mine, off the top of my head...
First, as someone who has tinkered with team ratings systems for many years, it is a firm belief of mine that any credible team ranking system has to take margin of victory into account. In fact, if I had to choose only one factor to use in a rankings system it would be margin of victory, similar to Sagarin's "Predictor" system. I have compared many different systems, and I believe using margin of victory gives the best indication of how teams should be ranked.
I am disappointed to learn that margin of victory will not be a component of the new Top 25 rankings system. If you're only going to be using win% and SOS, that sounds very similar to the RPI, so I question why you'd have both RPI and Top 25 as separate criteria for seeding and selection, when they both seem to be measuring basically the same thing. It sounds like double-counting.
Second, like dalter, I'm leery of having Top 25 used as a seeding/selection criteria. Especially if team ratings and/or team prestiges are used in the ranking calculations late in the season.