When trading is worked out the data could be changed to fit the cases of both games. Check original name of Pokèmon, if match convert proper of receiving the Pokémon or convert to uppercase before trading.
I always wondered why that was not done in pearl also. And even if above can not be accomplished like that... there could also be an option for the name rater to override a traded pokemon's name. Openpoke will be opensource after all, and anyone who wants to upper/lower/mix their cases would be free to do so.
Of course this could all be blind useless guessing, right?
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