First of all, bring back the bank from Majora's Mask. Why it was removed, I don't know.
Skyward Sword, as JuicieJ has mentioned, was probably the best example of money management in Zelda. You weren't forced to spend much money to enjoy the game properly, but you still had plenty of incentive to spend it, and as not everything was cheap, it felt more rewarding. Contrary to his beliefs, however, I think there's actually quite a bit of room for improvement with the rupee system in Zelda. I can usually fully upgrade all of my items by the end of Skyward Sword, leaving little to do afterwards. So the issue is not so much resource management now as it is longevity. Skyward Sword nailed management pretty well, but it doesn't always last long.
An easy way to fix this is to create numerous ways to spend infinite amounts of money and get at least personal pleasure from it. A house, for instance. Link can buy a house and then decorate and build off of it to his heart's content, using his newfound money to expand it. Considering the Wii U has its own little "Achievement" system, doing various things with the house can unlock small rewards. One of my biggest suggestions is a "Forge" system where you can actually make your own weapons from scratch. If enemies were stepped up in difficulty and variety, players could mess around with various weapon designs and see which ones work best for each group of enemies. Then you've got a bunch of other smaller ways to spend rupees, like sending them as a gift to newbie players or using them to give power to a certain weapon. There are all kinds of ways to increase the longevity of the rupee system, and I believe Zelda should work on this next in terms of economy.