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)

Monster Hunter: pissing me off since 2010.







