Aphrodite I'd actually go so far to call Links awakening the better game. It had more ideas presented more clever. The step by step exploration was carefully designed and you had to put more thought into what to do next. What nostalgia goes: I had played them both as a kid. But to an adult gamer who had no Nintendo games as a child I would recommend Links awakening.
The point is, that there where more memorable games in terms of units. Of course they used to sell a lot of cheaply produced crap. Also not everything that looked good on paper actually worked in practice. But nowadays almost every game seems forgettable. After the induced hype fades away modern games are justly cast into oblivion. I don't think there will be much left what will be called "an instant classic" in 20 years... Since we have nowadays so many possibilities to become creative I'm irritated over the lack of innovation.