Hey now,
@Cristovao, sometimes the thousand year old ancient dragon IS the god.
Anyway, I think Wavelength sums up my feelings best. When it's a cop-out final boss who just shows up at the very end out of nowhere and is just like "now fight me!" superboss style god battle? Lame. and also, strangely anti-climatic. Whohoo, I'm fighting a god! A god who up until now had zero impact on the story? As a narrative conclusion it never feels very powerful; I'd rather be fighting the thing that was my antagonist all along.
Now, there's some games that don't play it that way. If your narrative supports fighting the gods or a god of your world - then run with it. If the antagonist through the entire game's one true goal was to become a god, then fighting that antagonist as a god WOULD be a suiting climax. If you find out the main antagonist was opposing the gods because of some legit reason (idk the gods of that world determined humanity a poison and were going to exterminate them) then joining forces with antagonist and fighting the gods at the end would again be a fitting climax.
It's all going to depend on your story. Remember that staying true to your story and the narrative you want to tell matters more than "doing something cool."
And as others have mentioned, make sure it's clear to the player whether or not this is satire on real world religion or just your narrative. Use fictional gods, don't follow any existing religion too closely, build your own and distance yourself from real life if you don't want to be accused of anything.