i noticed the same thing in phantom hourglass. instead of thinking in terms of doing circles on the edge of the screen (as they tell you to do in the instructions) i just think of it as doing two small, quick taps against any edge of the screen. LKM described it more accurately, though.
i guess Tingle's Rosy Rupeeland - like any game - isn't for everyone. but in my own experience, i haven't had any trouble with negotiation and i almost never reset the game. whenever someone asks for a certain amount, i just give it to them rather than trying to haggle and taking a risk. it's not that i'm lazy - it's just that the asking prices always seem fair. and when i offer an amount for something, i just think in terms of being fair rather than in terms of trying to be a miser. and i almost never have a problem. after a while you just get a sense of the right amount to try for different things. it's not just random. there's a consistency to it. and there are also clues at the bottom of the screen when you have the misfortune of making a bid that's too low. a note at the bottom will say "50 more" or "500 more", letting you know that you should beef up your bid by that amount. so theoretically, the most you could EVER have to pay for an item would be twice it's value. and that would only be if you were extremely unlucky. i do sometimes have to make a second attempt, but i haven't had a hard time earning rupees in the game. i've found that i always seem to have exactly the amount that i need.
i make a point of going back through all the world's on a quick run-through with a bodyguard in between major dungeons or when i nearly run out of rupees. that way i get to add one more bodyguard to my database and i end up earning a couple thousand rupees and also filling my coffers with diverse ingredients. then i go back to town, do some cooking, sell the results, feed the tower, and hit the next part of the game. occasionally there's been a new item that came up for sale suddenly and i didn't have enough money. so i just spent a play session doing the above an extra time, which meant some extra money went to the tower as well as towards buying the new item. and as a result, after i win a major battle and get a bunch of rupees, the prize money is almost always the exact amount i need to raise the tower.
if you don't like earning rupees intermittently and you prefer to be constantly moving the main storyline along as quickly as possible, i could see where you might get irritated by the negotiating and feel stressed about conserving every last rupee. but if you are someone who likes RPG's and you look at the game from that angle (with earning rupees and ingredients being analogous to building up levels and buying new equipment) then the game flows perfectly. :-)