New games I've tested.
Ace Combat Assault Horizon Legacy (+): Drastically reduced loading times, and the framerate stays locked at 60fps the majority of the time. 804MHZ mode may perform the same as the new 2.1.0 version, I haven't tested the new update.
Pokémon ORAS: Mild improvement, after checking this and XY again, I can confirm that playing with 3D on is fantastic with very little drops..... On 1vs1 battles.
Project Mirai: Mild improvement. The animations are better, and there's less frame drops, but the loading times are still bad.
Also, fun fact: Xenoblade 3D runs like crap at normal 3DS speed, I'm talking about 5-15fps. It's practically unplayable. No wonder they didn't release it on old 3DS.