I think there's a zelda with infinite rupees, ah yeah it must be four swords, I think.

Khuutra: That’s possible, but you would run the risk of having the player run out of money and be unable to progress through the game. Would you rather make items limited in supply, or make them non-essential?

I personally think it might be good if the amount of munitions available in the field was absolutely limited, and rupees were made scarce. Then shopping/preparation would be meaningful, particularly if there are no drops in the dungeons…

On the topic of Rupees, i think The Wind Waker did it well, both in terms of giving you enough carrying capacity throughout, and in giving you a reason to have them (even if that reason was Tingle and those damned maps)

Majora's Mask also excelled in that area, though again with a few annoying things you shouldn't have had to spend money on (Curiosity Shop)

Face Shrine was very frustrating, which was partly my fault because i ended up going the wrong direction and got to the boss' door before i had the key, the beak, the map, or the compass, and kept running into a missing small key in that direction, and it took me a while to remember trying one door i had missed way on the other end of the dungeon. Frustration was ramped up by tough rooms that they forced you to repeat, mostly dominated by Wizzrobe, but one room with a pair of Dodongos was also repeatable

Topped off with an unsatisfying boss. Stand in the corner with your shield up until it runs out of tiles and pots to chuck at you, then stand on the face and place bombs to win...

I think that would be a welcome improvement.

Another random thought:

The Zelda series, since Ocarina of Time, in my opinion, does an extreme disservice to the awesome bosses that you fight at the end of dungeons.

They're total pushovers.

These bosses take very little to no damage (a quarter heart shouldn't even be a measurable damage count) and once you've discovered the pattern (which is never much a challenge), they fall like a ton of bricks.

I think it would be awesome to have boss fights as involved as, say, a hunt in Monster Hunter. Or at least have the bosses take significant damage and change up their attack scheme during the course of the battle more often to keep the player guessing. Seems Skyward Sword's sword fight battles will fix this to a large extent.

I've been saying Monster Hunter for a while now, though i wouldn't want a 30-50 minute fight. 10-15 might be good

Basically make them as strong as, oh, Gigginox or that rat bastard Rathalos, but only take as much punishment as Great Jaggi early on (who still falls quickly, but it takes you still 10 to 15 minutes of engagement)

I don't mind there being a number of rupee chests in a dungeon, but Twilight Princess wouldn't even let you keep them if you had a full wallet (which is basically all the time) which meant I had to go out of the dungeon, spend some money and come back in just to get the chests off the dungeon map.

Oh, and I am up to the doors of puppet Ganon in WindWaker, but have not yet gone through them (I am continuing to complete the Nintendo Gallery, and I am still missing 2 treasure maps from somewhere, but I can't recall where (which means it's likely something I haven't done on Windfall)

I thought about that issue. Naturally the dungeon and item design would have to be adapted to the new system. Even today, many Zeldas suply the player with "natural" bombs where they are absolutely needed. Why can't you have a system where the player is forced to resort to the weaker slingshot (with easily renewable amunition) if he/she runs out of arrows? Furthermore, there are examples of limited "special" munitions (bombochus, power-keg). History shows you can offer a limited avaliability of an item, and have said limitation make a real impact on the way you play, without completely impeding the player's progress.

You are correct about other potential solutions, though. I quite enjoyed The Minish Cap's endgame. Of course, it's still symptomatic of the fact that there just isn't a good use for rupees - it's a shameless money sink, just as Tingle and Malo Mart are - although the quests/rewards in this case are actually worthwhile.

On the subject of boss battles, I think bosses should epitomize play up until that point, both in terms of knowledge (strategically) and execution (tactically). Recent Zeldas rely almost soley on knowledge - know how the items work + learn the boss weakness/pattern - and do not require skillful execution. Majora's Mask actually found a balance - you had to master Goron rolling to beat Goth - and I wouldn't mind more of that.