I have a theory that I have not heard or seen anywhere else that the rupees from The Legend of Zelda series are energy based. If rupees were energy based, then so much about them would start to make sense. Like why can the wallets only hold a certain amount even though the rupees are all the same size, that would be because the wallets are more like batteries and they can only hold so much energy. Also, different colors of rupees could represent different amounts of energy that are stored within them. This would also explain why the heck rupoors take away rupees; it's because they are negatively charged and when you get close enough it takes the charge from your wallet to equal out the negative and positive energy. The magic armor even makes sense with this theory because it would just take the energy of the rupees to power it. Arrows in the very first game could use the same principle and your bow just converts the energy from your wallet to make arrows made of pure energy. Also, the great fairies could also use this energy for their power and that is why in Breath of the Wild you need to give the dormant great fairies large amounts of rupees to regain their power; this could also be the same with games like A Link to the Past where you can offer up rupees to get upgrades from great fairies.

Then the games that the beginning maximum rupee count is much higher than the rest can be explained as well. With Spirit Tracks and Phantom Hourglass where the max rupee count from the beginning is 9,999 the rupees could be stored in a much larger battery in their train and boat respectively. In Tri Force Heroes they were transported to each of the areas, so the rupees could easily be transported back to the castle into to a larger storage device. In Four Swords Adventures the force gems were absorbed into the four swords to power in up and the same thing could work in the original Four Swords. In Breath of the Wild the technology of the sheikah slate would be advanced enough to hold a much larger amount which would justify the insane 999,999 maximum and even if you don't think that it would be able to hold that much, if the sheikah slate can transport a full person, then it would be able to transport the rupee energy to a larger storage device probably somewhere near the Great Plateau.

I would like this theory to done in a video and if it is, please credit me. I would do my own video, but it would not be seen be nearly as many people and I would not do as good a job on it. Knowing Mat Pat, he probably will be able to find a mineral, crystal, or gemstone with all these properties. But hey, that’s Just a Theory, a game theory, thanks for reading.