while there is some story to be told, there just isnt enough to make a full game imo.
We can't really judge that for ourselves. If there was a story, they can make it work to fit in a full game if that was what they wanted.
all i can think of for gameplay would be aqua roaming the realm of darkness
Where Aqua could then discover a huge threat growing within the depths of Darkness, something more threatening than Xehanort himself. That's at least one idea they could go with. The worlds themselves would have been devoid of people, but who knows what else lies in the Darkness besides the Heartless. There is so little we actually know about the Realm of Darkness. We know it is where worlds swallowed by the Darkness go, we know it is where Heartless are born and deep within the realm is Kingdom Hearts.
But why is time distorted in the Realm of Darkness? How does Darkness corrode the heart? Are there people who willingly have travelled into the Realm of Darkness?
a minigame with apprentice xehanort doing research
Minigame? Not really sure how a minigame with research could work? Something like puzzles and quests that would have to be done to unveil the discoveries Apprentice Xehanort made during his time in Radiant Garden.
maybe something about the fall of radiant garden
There's ten years between BBS and KH1 that remain, for the most part, unknown. Who knows what happened during that time. Then we still have what uncounted events between KH1 and KH2. What was Riku doing during those gaps besides the few things we're aware of. We saw fragments of things we'd never seen before in Re:coded, but it wasn't enough to make heads or tails of what exactl
maybe it could be made as some other form of media though, i.e. manga, miniseries on tv, etc.
Or whatever they might have had panned could just be integrated into KH3, or even in a game post-KH3. Of course it will be different from what they probably planned but it isn't that hard to find a place for it if they really wanted to make the game and share that story.
Also the manga don't follow canon so they wouldn't really put something like that in them. Maybe in a novel since those are considered canon on some level, but it isn't an ideal direction to take considering the novels are only available in Japan at the current time.