When you go inside the cave, the puddle is based on the map of Sinnoh. The dots form a triangle representing the Lake Pokemon. Mesprit to the southeast. Uxie to the North. Azelf to the Southwest.
Sinnoh is peak of Pokemon lore. They thought of every stupid little detail. Also the piano music...
https://www.youtube.com/watch?v=96qogC-0VjI