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I've finished selecting all of the MIDI files. Here's what I decided to leave alone:
>Game Freak Logo: Too insignificant
>Main Menu: It's like, a five second loop
>Professor Oak's Theme: It literally only plays at the part where it's too dangerous to go into the wild without a Pokémon.
>Shithead's Theme: Gary Motherfucking Oak's theme is too iconic.
>Battle Victory Themes: Short and insignificant loops.
>Pokémon Center/Pokémon Network Center: Too iconic and I didn't have a good replacement idea.
>Encounter Themes: Insignificant, except for Team Isis's. See below.
>Lesson TV Menu: Another five-second loop.
>Jigglypuff's Song: Fanfare.
>Come Along: No ideas, iconic, insignificant.
>Lavender Town: Iconic to a memetic extent, and the only good replacement idea is Spooky Scary Skeletons, which I already used for the Pokémon Tower.
>Pokéflute: Fanfare.
>Sevii Island Themes: I just didn't feel like replacing Johto themes.
>Minigame themes/Union Room/Mystery Gift: No multiplayer means these aren't even accessible.
>Deoxys's Encounter and Battle themes: Due to already-implemented Deoxys event, I'm really not sure what we're going to do about the Birth Island event accessible by Aurora Tickets sold in Failsafe Cave.
>Champion Theme: Simply too damn epic to change.
>Hall of Fame and Ending: I did change the Epilogue to fit the altered Pallet Town theme, but other than that, just didn't feel like it.
>Fanfares: Not right now.
EXTRA NOTE: The Team Rocket encounter theme should be replaced by the unused G/S Team Rocket encounter theme that should be in the game's files from RS.
Finally, if you have any ideas to replace the themes I didn't, feel free to reply, and I'll try to find a MIDI file to send to OP.