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If I try to save after opening the PC, even if I don't change the PC at all, it takes a lot longer and says "Saving a lot of data..." instead of the usual "Saving...". It doesn't happen in any other game that I've played. Why do only DPPt do this? Please don't question my curiosity.

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According to Bulbapedia:

In Pokémon Diamond, Pearl, and Platinum, the usual "Saving..." message is replaced with "Saving a lot of data..." if the player has used the Pokémon Storage System at all during their session. This includes capturing a Pokémon and sending it automatically to a Box and using the Pokémon Storage System directly. It also occurs when saving and there is no save file already present. When this happens, the process will take significantly longer. In Pokémon HeartGold and SoulSilver, the message only appears after a Global Trade System trade, if the player is saving with no save file already present, if the save file is corrupted and the player is saving with a backup save file, or major changes are made to the Pokémon Storage System.

Sorry for just copy/pasting but I think this answers your question well enough on it's own.
In addition, as to why this is only in Gen 4, if I may quote Bulbapedia again:

The long saving periods of Generation IV have been rectified by giving the player only eight Boxes in the Pokémon Storage System until each one of the eight has at least one Pokémon in it, avoiding the need to encrypt empty Box data. If major changes are made to the Pokémon Storage System after all the Boxes are available, the "Saving a lot of data..." message appears, and saving will take longer than normal like in Generation IV when this message is shown.

If you want to read more about this you can view the Bulbapedia article in full here.

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By any chance do you know why it takes so much longer than it does in Generation 3?
I did some research and found out that a lot of people ask about this. It seems that some people have more of a problem with it than others. As to why, the only thing I could find was somebody saying that the Gen 4 games have a much larger save-file data than the other games, and the flashcard you have in your DS can impact the amount of time it takes to save. I'm not sure about the legitimacy of this claim, but it makes sense.
Also, you may want to check to see if any of your other questions about this have been answered here: https://pokemondb.net/pokebase/130626/what-causes-the-game-to-save-a-lot-of-data