The only Zelda game I think did poorly on the rupee system was WW. Most of it was fine, but when the Tingle Map quest forced you to collect loads amount of rupees, it took away from the joy of collecting rupees. Most Zelda games, including SS, use rupees as a convenience. In the past, rupees were only majorly needed for collectors or serious Zelda players. You could go into battle without the things you needed rupees to get and there was rarely a major item you needed them for. SS differs in that while everything is still optional, (thereby not taking away from the joy of collecting like WW did) the things rupees provide you like upgrades and newer shields are more... valuable to the casual user, making rupees themselves more valuable. You don't have to buy these things, but you want to and there's ALOT of things you want to buy. This system is not better nor worse in my opinion. It makes rupees feel more like currency, so if that's what you were looking for than SS provides, while (as previously stated) making them more valuable and the statement "a rupee saved is a rupee earned" all the more true. However, I simply had a more enjoyable time when rupees were used by the experienced player. Made me feel special in that I knew how to correctly use my rupees and what to use them for.
All in all, SS makes rupees more valuable and more like currency. Not a bad idea, (a good idea actually) just one I Personally don't like as much as previously used games.