I think one of the worst mistakes that any creator can make is not knowing what it is they want their work to be.
And I don’t mean “I don’t know where my story is going”. You can actually write an entire story without having a solid idea of how it will end.
But what you do need to know is what your game IS.
For your story, you need to know the tone you want to project. Now, you can vary a little bit here. Just because you want to make a serious story doesn’t mean there can’t be jokes, but the jokes need to fit into the whole. Embrace the tone you want for your story! Even if it seems “low class”. If you want to make a campy game, MAKE A CAMPY GAME.
Don’t waffle about it until your entire game is an incoherent mess of tone and storylines.
And the same goes for gameplay. Figure out what you want your gameplay to BE. Is it meant to be simplistic and casual like an early JRPG? Is it meant to be complex and reward mechanics mastery like modern Diablo-clones?
Is there a theme in your gameplay? Are you purposefully playing with scarcity of supplies in order to communicate to the player? Are your mechanics made to emphasize the friendship of your party?
Then make sure that when you are adding mechanics to your game, that they are fitting into the overall plan you have for what your gameplay is!
And on top of making sure that both your story is coherent, and your gameplay is coherent, you also need to make sure that your story and gameplay are coherent with EACH OTHER. If you are emphasizing the friendship of your party in the gameplay, that should also be a part of the story as well.
Everything should revolve around figuring out what your game IS. It’s such a nebulous concept to be honest. But once you grasp onto the identity you want the game to have, a lot of other things will fall into place around it. So find the identity of your game. And make sure that it is designed around that identity.