OK, this response is super late (I know you posted this a month ago, and you've probably navigated this issue since then), but maybe this can still be useful to you or someone else looking for help on this topic.

I think for a beginner who is struggling to balance gameplay and story, this method could be useful (certainly is for me!):

1. Identify two things: what style of gameplay, and what the gist of the story is. Keep things simple - "match-3 about animals" will be our example here, but other similar pairings could be "traditional RPG about lawyers" or "driving/racing game about romance". Even if you have a complicated idea in mind, dumb it down to figure out what the core of the game is.

Result: "Match-3 puzzler about animals"

1. Slowly expand both concepts in a roughly independent manner - the gameplay with features, and the story with plot. Keeping them 'separate' here (just barely) forces you to think about the game as two things - fun to play, and interesting as a narrative. Don't get too big yet.

Result: "Gameplay: match-3 with contextual combos. Story: Animals being sold in a pet store."

Your brain is probably already churning with little ideas from step one - jot them down!

1. Twine both aspects, gameplay and story, together - still trying to keep things simple. Describe the game like you would to a friend you're trying to convince to play the game for the first time.

Result: "You play as a pet store owner trying to sell his animals, in a match-3 puzzle grid format. As the game progresses, contextual/trickier combos can be made to increase your score. Sell (match) three cats and three mice side-by-side for a 'Tom and Jerry' combo, or put a snake between a lizard and a fish for a 'Scaly' combo."

1. *Keep adding features/plot, but ensure they are balanced and ideally linked - even if it's just adding some story to justify/explain the new feature.

Result: "Linked concept - Feature: In some stages, animals come in male-female variants, and there is a 'breeding' combo - dragging a nest between a blue and pink bird makes chicks, which are needed as part of the level goal. Story: The store owner is running low on stock as his business booms, and starts to breed his animals to increase stock."

You might find it easy to write out a list of features and a list of story elements, and see if anything seems to click together. Sometimes they will go hand in hand and seem really obvious - a bulletin board for adopting strays (story) naturally goes well with a daily challenge system (feature). These are the best ideas - because they seem natural and logical to you, they'll probably be natural and logical to the player learning that mechanic. Don't wrestle to make something work if it doesn't fit!

1. When you have a game described with many interesting features and a great story/plot to compliment it, break it down into a concise outline or use it as a basis for your GDD.