Haven't tried open_agb_firm yet? It works exactly like GBA's VC (GBA games run natively on the console) and it has its own scaling method. Maybe you like it (or maybe you don't). It's still WIP, so it might get better for you later on.
I've checked out that thread, from what I've read it still uses 1.5x scaling but with a sharpened interpolation, while I'm being rather picky and would prefer 1.25x scaling (which is how GBARunner displays GBA games since it's displaying GBA games 1:1 in DS mode, and the DS mode image is upscaled to the 3DS screens so it's a 1.25x scale from the original GBA image). Good to know there's some work being done on AGB_FIRM though