I think the Zelda team did great handling rupees in Majora's Mask, Wind Waker, Minish Cap, Phantom Hourglass, and Spirit Tracks. The limits were 5099 (bank), 5000, 1000 but had ways of spending money, 9999, and 9999. I felt like I always NEEDED rupees in those games. Kinstones, Triforce Charts, Chart deciphering, ship parts, train parts, collectibles, secret seashells, sidequests, bank rewards etc.
Twilight Princess was the only recent game that handled the money badly. There was not enough to buy and the rupees came easly, plus the limit was a joke and the fact that they made you keep rupees in chests if you were maxed, meant you had more useless money to waste. Skyward Sword needs a good rupee limit like 5000, or even 10000, and there needs to be collectibles or rewards that make you need to spend your money, and even search for money like in WW when you had to decipher all the charts for 980 something rupees a piece...
As for the rupees going into the pocket. I don't think you you want the Zelda team to throw a gigantic leather backpack the size of an elephant on Link's back. So lets just say, thank you fiction, and be done with it.