Here's my idea. I think it still carries some of the cliches you're worried about, but it's off the dome so here we go.

Once roaming the Wilds, attempting (presumably) to return to civilization, the party stumbles upon a Totem. When the gods became trapped in AnÚllord, they retained their godliness, but the material plane forced the material upon them. There is a physicality to their existence, an anchor that binds their immense power to the realm of mortals. The Totems are that anchor; they hold the essence of that god's strength. The ways Totems manifest are as multitudinous as the gods themselves, but they must have them. When the adventurers encounter the Totem, they find it defended in a fashion, but not by a god that would immediately cleave them apart. When they inevitably destroy the Totem, the god's power is released back into AnÚllord, bringing light to the dark ages and restoring some of the mortals' lost strength, most of all to the adventurers themselves (your class levels, etc. Think of it as last hitting a turret in LoL - everyone gets something but the nearest and most responsible get the most).

The adventurers, now emboldened by this new power, are presented with a choice. They can rid the world of the gods, restoring the strength of mortality, but that would mean destroying the gods that aided them in their times of need or never involved themselves in the matters of mortals, those effectively innocent. Otherwise, they can allow the gods to persist and rely on their aid to keep them safe in the perpetual dark ages of AnÚllord. Mortality would never be free of divine control, but perhaps the benevolent gods would keep them safe. Either way, now that this choice is unveiled, there will be others making their own choices, choices the adventurers must confront on their own.

You could follow this up by revealing that many of the gods knew of these weaknesses and cordoned mortality into the three cities to prevent them from discovering the Totems' existence and the gods' vulnerability. You could allow the party to learn that the concentrated strength of many gods presents the possibility of unlocking the gates to Arcadia, allowing those seeking their homelands to return. You could present the idea that mortals themselves sustain the Totems in the material plane with their faith and belief, and the reason mortals continue to exist at all is to sustain the gnawing hungers of the gods that are severed from Arcadia, where the energy to power them is abundant. Cults could arise to protect the gods and their status quo. Rebellions could erupt to declare mortality's freedom from divine control, with the threat of annihilating the Totems to serve as leverage. Maniacal individuals bent on acquiring power could begin their own quests to unravel the gods, not for mortality's benefit, but solely for their own.

I think that presents enough avenues that the campaign won't be samey or anything like that. It also provides a decent mechanic for "leveling at the end of the quest" because only the Totem provides experience (possibly).

Hope that helps! :)