Well, you certainly aren't the first person to question the differences in shifting between a newer Pilot and an older one - check out this thread from last year
Tranny impressions - 04 vs 06 . And here's a specific string about the gearing differences.
Gearing differences - '04 vs '06
Overall, my mpg is 2 lower than my wife's in similar driving. Shifting hasn't changed on the '06 after 15k miles, and the MPG hasn't changed either. Definitely a more "sporty" and "responsive" feel in the newer models than the old, but you pay for that in lower mpg....
andy