>>42453321 (OP)
Re-do the characters to be less cute and write the human world to be less wholesome. Teenagers are jerks and high school is shit. Anyone who had positive memories about it had to make them in spite of.
Both Twilight and the Mane 6 cross the portal without losing their horse form, teaming up with their human counterparts and having fun shenanigans along the way.
Make the high school a small part of a bigger setting (like a metropolis), so they can explore cooler places and the final conflict feels much more impactful.