Megabeasts don't really "take the place" of Gods - as far as I can tell, people worship dragons as gods because that way, the dragon doesn't eat them. Worshippers elevating dragons to Godhood status always seems to follow rampages in the town where some of the worshippers were directly injured by the dragon, and started worshipping the dragon after being spared death by the dragon.
So you have things like dragons and titans, which are worshipped as Gods, even though heroes can defeat them in single combat, sometimes even with a single blow.
I'd rather see something where the sphere system is upgraded, and we get Gods that are directly related to their spheres.
If we're talking about the stuff VoidPointer was talking about, maybe Gods are born when someone creates an artifact idol, and starts worshipping it. (Older gods might also be mortals that ascend... maybe even the original dwarven Gods are simply the patriarchs and matriarchs of dwarven society, worshipped to Godhood.)
This means that we could tie the powers of a God to their degree of worship, as well as their sphere. They could, for example, start out with basically being a mortal creature of the type that they are "most often portrayed as", and get bonuses for the degree of influence their sphere has, plus the number of worshipers they have.
This can also lead to Gods having powers that spread their influence through any land with their sphere, plus having the sort of god-to-god conflict over worshippers.
Of course, then we might want to consider having deities with relationships with one another. Whether it be parent/child relationships like most of Greek myth, or conquering lord/servant relationships, where a weaker god is allowed to live as a servant, or a lesser partner to a more powerful god, or even just outright drinking buddy gods (Thor and pre-Christian revision of Loki).
(That way we could have, I don't know, a Goddess of the Mountains and a Goddess of the Sky living together after the Goddess of the Sky defeated the Goddess of the Mountains, where the Sky Goddess plays a front woman, gathering faith, while the Mountain Goddess works on making the miracles the Sky Goddess promises, and they could live together with the Mountain Goddess's great-great-great^92-granddaugther, who's also their High Priestess.)