I think a large part of the problem is how people run. My friends who always grabbed random games and did it with a full group were still getting comparable drops. Possibly because the effect of weaker monsters and stronger players which Cujo pointed out has more impact here.
However for players such as myself who do the runs solo, there is a huge change. While perhaps runs are slightly faster now, we're talking about 10-12 minutes instead of 12-13 for most melee classes doing a solo rush. Previous to season 3 I'd be getting around 20 frags for a full Gaikoz *** run. Now post Season 3, while trying to do Mari's 2nd job, I was doing runs (pre-revamp) and getting 3-4, for a full run. After the revamp it got even worse, now doing every room (as if there's a choice) I was lucky to get 2 frags, and the time still wasn't that much quicker. Overall, I'd say the total time to complete a second job quest for me has gone from ten hours of running gaikoz to somewhere around thirty-five. Even at 10 minutes per run, getting 2.5 frags average, you're looking at 20 hours, not including time in between runs, loading screens, end screens, and time not playing.