UtopiaNextworld

Manaphy in pokedex is number 151 because of this number is written on a message file where pokedex strings are. Find this string on your rom (dumping your pl_msg.narc as a text file using TheNewPoketext), and you may be able to edit it then.

In PPRE, you have a hex value (0-255) for each trainer pokemon. The value there mostly corresponds to IVs (255 = 31 IV across the board for example) but the nature of the Pokémon is set by some combination of the IVs, level, species. There doesn't seem to be any rhyme or reason to it. It's likely to be linked with the Pokémon PID but not sure about this. So yeah, it's just trial-and-error, changing the number each time and catching the Pokémon with an AR code to check its nature. Very tedious stuff sadly, but there's no specific way to set the nature. That's more or less what Dray told me when I asked him. What to do then is setting a NPC in Overworld, with a script throwing the trainer battle you want to edit and then working on trainer nature with AR-Codes (catch trainers' pokemon + 100% catch-rate).