I'll be okay with a system that puts some kind of (tiny) restriction on their powers

In that case, have the three differently ranked in terms of priority. One of them is truly omnipotent, however the second is omnipotent as long as he doesn't oppose the first one and the third is omnipotent as long as he doesn't oppose the first two.

or

The gods are all omnipotent, except when opposing another. So a god can't stop another god from doing something, but can undo it afterwards. And a god can't make his effect unundoable by another god. So if one god wants to make the weather baking heat, while the other wants a storm, one must wait until the other is finished creating the storm before taking away the clouds and wind and turning up the sun.

This, of course, may result huge chains or stacks of effects to "resolve" á la Magic: The Gathering. But given that each one is instantaneous, even such a stack trillions of effects deep would not even be noticed by the mortals. (Or maybe it would... cue the mortals rolling their eyes, "the gods are at it again...") -

Maybe in the case of a deadlock, the third god casts the remaining "vote".

The possibility that all three could want something different and remain steadfast could be a plot hook.

or

Gods with infinite wisdom also have infinite maturity. Therefore they can always come to an agreement on a way to resolve their differences!

I'll be okay with a system that puts some kind of (tiny) restriction on their powers

In that case, have the three differently ranked in terms of priority. One of them is truly omnipotent, however the second is omnipotent as long as he doesn't oppose the first one and the third is omnipotent as long as he doesn't oppose the first two.

or

The gods are all omnipotent, except when opposing another. So a god can't stop another god from doing something, but can undo it afterwards. And a god can't make his effect unundoable by another god. So if one god wants to make a storm , while the other wants a baking heat, one must wait until the other is finished creating the storm before taking away the clouds and wind and turning up the sun.

This, of course, may result huge chains or stacks of effects to "resolve" á la Magic: The Gathering. But given that each one is instantaneous, even such a stack trillions of effects deep would not even be noticed by the mortals. (Or maybe it would... cue the mortals rolling their eyes, "the gods are at it again...") -

Maybe in the case of a deadlock, the third god casts the "deciding vote".

The possibility that all three could want something different and remain steadfast could be a plot hook.

or

Gods with infinite wisdom also have infinite maturity. Therefore they can always come to an agreement on a way to resolve their differences!

I'll be okay with a system that puts some kind of (tiny) restriction on their powers

In that case, have the three differently ranked in terms of priority. One of them is truly omnipotent, however the second is omnipotent as long as he doesn't oppose the first one and the third is omnipotent as long as he doesn't oppose the first two.

I'll be okay with a system that puts some kind of (tiny) restriction on their powers

In that case, have the three differently ranked in terms of priority. One of them is truly omnipotent, however the second is omnipotent as long as he doesn't oppose the first one and the third is omnipotent as long as he doesn't oppose the first two.

or

The gods are all omnipotent, except when opposing another. So a god can't stop another god from doing something, but can undo it afterwards. And a god can't make his effect unundoable by another god. So if one god wants to make the weather baking heat, while the other wants a storm, one must wait until the other is finished creating the storm before taking away the clouds and wind and turning up the sun.

This, of course, may result huge chains or stacks of effects to "resolve" á la Magic: The Gathering. But given that each one is instantaneous, even such a stack trillions of effects deep would not even be noticed by the mortals. (Or maybe it would... cue the mortals rolling their eyes, "the gods are at it again...") -

Maybe in the case of a deadlock, the third god casts the remaining "vote".

The possibility that all three could want something different and remain steadfast could be a plot hook.

or

Gods with infinite wisdom also have infinite maturity. Therefore they can always come to an agreement on a way to resolve their differences!