The Battle Tree Boss theme might be the best in this series to me. It's a combined remix of Red and Blue's themes from the GameBoy, but it sounds like a completely new song with how they arranged it using modern instruments. You might not even recognize all the similarities when you first hear it. It is perfect for the boys coming back as adults.

Zinnia's theme is way too good for how short and easy the actual fight is. Smash 4 has a nice remix of it.