An old and wise Pokemon professor could also be a main character. He might be the one who first discovers the existence of the worm - like Pokemon or the concept of the crossover. He then guides the young trainer in understanding and caring for this new type of Pokemon, using his vast knowledge of Pokemon biology and history.
A young and curious Pokemon trainer would be a great main character. This trainer could be someone who is always on the lookout for rare and unique Pokemon. When they encounter the worm - like Pokemon, they are immediately intrigued and decide to make it a part of their team.
The worm - like Pokemon itself could be a main character. It could have its own thoughts and feelings, and be on a journey to discover its place in the Pokemon world. Maybe it was born different from other Pokemon and has to face challenges because of its appearance and abilities.