Shoehorning the Master Sword into every Zelda game just isn't right, even when considering the official timeline, it doesn't make sense having the Master Sword, in neither Zelda 1, and much less Zelda 2. There's many reasons why (and this is coming from someone that has hacked and researched many games in the franchise).
In Zelda 1 you get basically better swords from NPCs, and they have no impact nor are required to defeat Ganon/final boss (unlike all other games where you obtain it). Only the Silver Arrows are needed.
In Zelda 2 you don't even get another sword. The same one you start with is the same one you keep until the end (which is assumed to be the Magical Sword from Zelda 1).
1) The swords you get aren't found in a pedestal (all other games with the Master Sword have it in one) or requires the hero to prove it is worthy of it.
2) The upgrade swords are 100% optional, you can even beat the game with the starting wooden sword, while all other games with it make it a focal plot point of the story.
3) At this point in the timeline, Link failed against Ganon, even with the Master Sword, so it makes sense other methods are being used to stop him.
So yeah, give other different swords a time to shine, not everything has to be the Master Sword just because it's a Zelda game.
If I may, and more of a suggestion to the person making the HD pack, I'd suggest making the sword in Link's sprite a bit larger. It looks too short (like the original, but even in there it didn't look good). At least making it a coupke pixels larger and a bit less chunky might help a lot.