Zelda Majora's Mask. The waiting for certain events is annoying, because you can only fast forward between day and night, but not to certain dates. Oh, and N64 graphics obviously.
They fixed both in the 3DS remaster, but made so many other things blatantly worse, it sucks. There's lots of things you can give Nintendo shit for, but fucking up Majora's Mask is easily the most irritating thing they ever did in my book.