The real answer is that obviously that the developers never thought about it in the past, at least not as part of the story and the same way its done in SS
Now, if you want some explanation for the world in the games, then as many have said, it would have something to do with Fi or Demise.
But adding something to the theory, [EVEN MORE SPOILERS!] when we fight Demise, we are in a battlefield created by Demise, and when we are battling here its the only time when the sword cant do skyward strikes, because the power of the Goddess is negated. This may help to explain how Demise in the Master Sword can negate this power or that the Goddess power has disappeared/has weakened/cant reach the Master Sword
Now, at the beginning of the game we are asked to rise the sword so it can be bathed by the sacred light in the chamber of the goddess sword, maybe this power faded.
Why the sword can do a Sword Beam in ALTTP? I can think about two theories:
Skip to 1:05
Link pulls the master sword and rise it skyward, then the sword shows lighting
The other theory lays in the difference of how we do skyward strikes in ALTTP and SS, in skyward sword we can do it almost at any moment (the only time we cant is already mentioned) by rising the sword, the way it works is probably so we don't spam sword beams, it would be to easy that way. But in ALTTP and in many other games, the sword beam can only be done when we have full health, link need to use his own strength to activate the power.
Now, the Ether Medallion in ALTTP reminds me of the fight with Demise
Skip to 3:30
I think the master sword did have the ability to use the skyward strike they just didn't know. I was finishing the legend of zelda oot again and noticed that at the end of the game before he kills ganon his sword lights up blue, could this be fi's power?
*EDIT*
http://www.youtube.com/watch?v=KhVyHRlEN14
skip to 2:35
You have two interesting points, no one has explained link how to use the skyward stike, maybe XD. The other is the blue light with the MS at the end of OoT, seems like an interesting theory