It is interesting to look at the NPI vs. the PWR (which can still be found on CHN if you dig a bit).
1 seeds: The same across both systems. Michigan is #1 in both, Western Michigan is #4 in both. NoDak and Michigan State flipflop between 2 and 3.
2 seeds: Both agree on the TEAMS in the 2 seed block (Penn State, Providence, Quinnipiac, Denver), but the ordering is different. PSU is 5 in both, the NPI then goes PC-QPac-Denver, while the PWR goes Denver-PC-QPac.
3 seeds: Cornell, UMD, Dartmouth, Wisconsin in NPI. UMD, Cornell, Dartmouth, Wisconsin in PWR. So, minor shuffle but same teams.
4 seeds: Both agree that BC is #13. Both have UConn and Augustana some combo of 14/15. NPI has Augustana higher. This could be the cut line though, with any bid thieves. Augustana is the highest rated CCHA team, and there is no AHA representative in either, so if Augustana DIDN'T win the CCHA but lost in like the tournament final, UConn could get edged out for that second CCHA bid. Obviously any surprise winner of a multi-bid conference could mix things up, too. The AHA rep will be the #16 seed barring something completely shocking, as Bentley/Sacred Heart are the highest ranked teams at around 30ish. The last team out in the NPI is Minnesota State. In the PWR? Your Maine Black Bears.
Once you get to 16 and lower is where the real differences between the PWR and NPI show up. Minnesota State is 16 in NPI but 19 in PWR. St. Thomas falls from 17th in NPI all the way to 24th in PWR. Bowling Green falls from 19th to 21st. I'm not a math whiz, but for some reason the NPI loves the CCHA a lot more than the PWR. PWR prefers Maine (18->16), UMass (20->17) and Ohio State (23->18).
I don't know that either is necessarily "better." At the end of the day we are parsing resumes of teams that are 18-12-3, 19-12-1, 18-9-7(x2!), and 18-11-5 (Maine, UMass, St. Thomas, Minnesota State, and Bowling Green). Ohio State is 12-18-2. Just win more games is the solution for any of them. It's not like the Pairwise has a team at 6th and the NPI has them out.