Caring about morality, having agendas that are in any way "agendas", rather than y'know, sexy urges, emotional outbursts, and general childishness? Not really my memory of the Greek myths. At all. I'm talking about gods that actually care about the stuff they're god of and actually interact with the setting.
I've always found D&D's peculiar combination of effective godhead and open pantheism fascinating, because it's pretty unique.
Moorcock's characters have the sort of conflicts you mention with the divine beings in his settings. They are certainly concerned with morality and pursue at least one major agenda. In the same vein the chaos gods of Warhammer are definitely agenda driven, although those agendas are not particularly complex. They are also all very selfish, however.
Fritz Leiber's Nehwon has thousands of gods, and you get the impression that worshipping several of them or blaspheming one or more of them carries little penalty, but by the same token they are not for the most part particularly powerful or relevant.
I don't think gods in fantasy fiction are particularly popular right now. We went from a pantheon being a setting staple (and obviously having a dramatic effect on the development of D&D) in the 70s to settings in the 80s and 90s where gods were being banished, exiled, and killed, and now they're just kind of passe.
Although baseline D&D has always suggested an open pantheism, you can see this progression in the specific D&D settings. Greyhawk and Forgotten Realms are traditional high fantasy worlds with gods like those you'd find on Nehwon or in Sanctuary. Then Dragonlance comes along and proposes a world where those gods had left for a time, by their own volition.
Then the Time of Troubles occurs in Forgotten Realms and the gods are banished from the heavens and made mortal -- some of them die. Then Dark Sun kills all its gods, Planescape opens a sort of "See the Houses of the Stars" tour of the outer planes, based in a city completely impervious to divine presence, Birthright kills all of
its gods, and Dragonlance sends all of its gods into self-imposed exile.
And finally, in Eberron, we have the first D&D setting where there are gods, but they never contact the world directly, relying exclusively on the granting of divine magic to make their presence known. Pretty sterile.
Golarion is, of course, a counterpoint, harkening back to the Greyhawk and Forgotten Realms design.
I suspect it is related to the secularization of society, but that's just an educated guess. You can definitely find the sort of gods you are talking about in fiction if you're willing to go back forty or fifty years, but it never quite looks like D&D. The need to accommodate players left its mark on D&D religion in a way that just isn't reflected in extant fiction.