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I using No$gba for playing some pokemon fine except working on PC inside Pokemon Center and Pokeathlon because the speed problem. So, Desmume is best choice for anything. :)
For me is doesn't matter which one choose just likes previous version of Pokemon. At very important is battle the GYM 1 which always rock type at all regions except Johto which you will battle the GYM at flying type.
What version of AR code are you using? AR version 1 & 2 or AR version 3? In VBA emulator, AR version 1 & 2 was not available and only use AR version 3 or later (use Gameshark button). For No$gba emulator, both AR codes was available now!