Regardless of whether an EGA version existed, the style of the sprites was already different. The sprites from SQ I, II & III belong to an earlier era -- hard to describe, but if you remember them you must know what I mean. More abstract & pixelated, designed for low-res and low-color displays.
They bring back memories! I don't want to wax nostalgic -- but I will anyway. I've come to think the more primitive/abstract the graphics, the more they engage the imagination. Similar to Scott McCloud's concept of "closure" from Understanding Comics, maybe? While playing SQ II, I could believe the world was enormous even when it was actually quite limited. In the jungle of planet Labion, I believed I was exploring a vast wilderness. Games with more realistic graphics -- even when they are sandbox games -- don't give me the same feeling anymore. Of course, I'm also older and more jaded, so there's that too ;)