If I understand right, you actually can find and extract the data of a pokemon in a save file of GBA games (anyway, let me know if you need help in this part, Bulbapedia have some information wrong or missed) and the only thing missing is how the game truly make the conversion to have a really legit NDS pokemon. Well, I plan to do some experiments for that, since NahuelDS spoke with me. I suppose what any information we find, could be commented, I hope that you make your own program, how I hope to make the me (in spanish, of course).
However, I don't understand why, you guys, make this type of programs separately, e.g. Mystery Gift Editor, 136 <-> 236 Pokémon Converter, Item Editor, etc. Why don't make its for the PPSE?.
PD: If you wanna throw a look to Enciclopedia Pokemon, you can use the translation of KazoWAR (I mean, if you don't see that): http://www.mediafire.com/?0gmiezri2d1