I made a comic about this very same issue, except pertaining to Mega Man instead of The Legend of Zelda, almost six years ago. Seeing as very few of the Links that appear in the various games in the series are actually the same Link, this can be easily explained. Now Mega Man, on the other hand, who is the same hero throughout his series cannot be as easily explained away. Nonetheless, it’s easy to understand why Capcom chose to follow this formula. They’re trying to avoid being Dragon Ball.
In the Dragon Ball series, as Goku gets stronger his enemies have to get stronger too. In episode 3 of Dragon Ball Z, Goku’s power level is 330. At this point Goku is arguably the strongest person on Earth. In episode 223, Goku’s power level is now 150,000,000… WTF?! That’s just dumb, but what’s even dumber is that his friends are comparable in their own power levels too. Sure Goku is still stronger, but the difference between their levels is not like the difference between 330 and 150,000,000.
So rather than dealing with the idea that Mega Man, or Link, has to continuously retain his abilities and strengths from the previous installments, the video game developers simply choose to press reset and start fresh.