The Late Philip J. Fry (the time machine one), as you admitted, was hilarious. They worked in references to piles of classic science fiction movies; the show covered time travel, theories of the nature of time and the universe, paradoxes, and predestination; and the writing was tight and funny. So we seem to agree that one was solid.
A Clockwork Origin, two episodes later, pulled together the panspermia hypothesis, the debate between intelligent design and evolution, the singularity, and clear send-ups to Second Variety and Planet of the Apes.
Proposition Infinity was more a political than a science fiction episode (and we had those in the earlier seasons, too--the garbage sphere, the women's planet, etc.), but I thought did a hilarious send-up of Proposition 8, religious responses to homosexuality, San Francisco gay pride parades, and so on.
And while I agree that episodes from this season are in general more vulgar than average from previous Futurama seasons, I also think you're viewing those seasons through rose-colored glasses. The sex in this episode was no more explicit than Fry and Leela in Tales of Interest, Professor Farnsworth's seduction of Mom in Mother's Day, or half a dozen other episodes, and while I thought the third episode of the season (Attack of the Killer App) was disgusting, I don't honestly think it was more disgusting than Fry and the Slurm Factory, where it's revealed that Slurm is slug poop.
Futurama's always mixed highbrow with lowbrow. I agree they've gotten raunchier, and I think it hurts the humor. But I think writing the whole season off as a loss is extremely unfair.