I am having an issue with the graphics in KQ5 and Kq6; they look EGA quality and not what I remember from playing these years ago. I've tried all the different graphic setup options to no avail.

That may be just because you haven't played them for some time. I remember KQ5 looking awesome in the early 90's when I played it too. But compared to today's graphics, it does show how outdated they are. This is probably what you are experiencing. Post a link to a screen shot of your gameplay so we can see. But I have a feeling all is fine.

Also, you can use the DOS version screenshots on Mobygames for reference.

KQ5:
http://www.mobygames.com/game/dos/kings-quest-v-absence-makes-the-heart-go-yonder/screenshots

KQ6:
http://www.mobygames.com/game/dos/kings-quest-vi-heir-today-gone-tomorrow/screenshots

Also, you can use ScummVM to play these games. This makes sure you play them as they are intended to.

Personally, I always use 2xSAI filter to make them less blocky.

I still think they look great, by the way.

This may be a bad example, but when I was a littlle kid, I remember all those shows on PBS and other type saturday morning cartoons; I thought they were really cool and awesome, but now I'm older and when I try to get interested, it's impossible because they just aren't the way I remember that.
The analogy is awesome and graphics. I'm not saying those games aren't awesome. It's... you know what I'm saying.

If this is any help, I've noticed that KQ6 is the floppy version. There is a significant enough difference between the two(eg. the character portraits) that I think GOG should make the download the CD version. Use this image and compare to it in the game.

What GOG offers IS the CD version, the DOS CD version. What you want is not the CD version but the WIndows version. If you want to play KQVI like that, install ScummVM and point it to the installation directory and choose the Windows version.
See these threads for more information on this topic:
http://www.gog.com/en/forum/king_s_quest_series/kq6_svga_graphics
http://www.gog.com/en/forum/king_s_quest_series/kings_quest_6_voices

Yeah, I figured the CD windows version thing AFTER I posted, which made me feel idiotic. :P