The way I see it, being a KQ fanboy/girl because of KQ6 is kind of like saying you're a Miles Davis fan but only owning Kind of Blue. 
Not everyone can live up to your high standards, I suppose 
I played KQ6 first (I had played 3 a while before when I was a kid but only at my cousin's house.) It was such an involving game that I just couldn't stop playing it. KQ5 may have been pretty and all, but the game was crappy --it frustrated me at best. Liking KQ5 over KQ6 is a matter of nostalgia and preferring King Graham, because there's nothing subjective about KQ6 being a better game. KQ5 is the perfect Sierra fan dream. But heck, any other King's Quest was better gameplay wise than 5. 5 is just very special in people's heart because it started the VGA era. I, on the other hand, experienced the start of the VGA era with SQ4 (which is why I love it so much).
Great music, very different characters, very different lands, a sense of the world as it was built by levels, two different paths to the end, a great love story, and exciting ending sequence that starts once you disrupt the wedding. What's there not to like?
Actually, I'd think there WAS something subjective about KQ6 being a better game. Art isn't something easily defined in any real objective sense. For example, an action gamer might argue the MERITs of action games over adventure games, but that doesn't make action games better in any real sense; simply better in his/her perspective.
I think saying that the only reason one would prefer KQ5 is "nostalgia" kind of belittles the people--Like most of the people over at IA, for example, myself, and others who DO prefer KQ5, and not simply because it started the VGA era. Personally while KQ5 is probably my all time favorite KQ game, I consider SQ1VGA one of the best games of the VGA era, after it coming Conquests of the Longbow.
Any other KQ game was better than KQ5? Really? So, the original KQ2 was better? KQ7 with all of it's non-interactivity? KQ8?
I would argue that KQ5 had great music and could even name many of the game's pieces of music which I feel outshine any KQ6 music. KQ5 also has a wild variety of characters--from the fun and bright to the dark and strange and everything in between. Serenia is one Kingdom, yes, but each part of the realm is VERY different from any other. One part of the land is a desert wasteland, the other a realm of ice and snow; There's the beach; the Dark Forest; the Harpie Island, and finally Mordack's castle--All perhaps the most fascinating places in any of the KQ games. Two paths to the end? Meh the whole multiple ending thing is kind of silly and reminds me of those "Choose Your Own Adventure" books. I think a story has one, definitive ending.
A great love story? I'm not a big fan of romance stories, personally. And for all the writing in KQ6, the love story could've been written better IMO. The ending? I find the whole ending of KQ5 to be exciting and thrilling--Silently searching around Mordack's creepy castle, in danger of being grabbed any minute by the Blue Beast, having to evade the eyes of Manannan and bag him, and finally that magical battle--For me the ending of KQ5 with it's almost poetic quality; Winged Creature against Lion; Dragon against rabbit; Snake against Mongoose; and finally, fire against water. It's almost poetic in that sense and it ends triumphant, yet not overdone. KQ6's best ending kind of reminds me of the "Mega Happy Ending" of Wayne's World.
I also feel the world in KQ5 FEELS larger than in KQ6. It may not be bigger by screens, but it feels like you're a little man in a large world. I always wanted to know more about Serenia, more about the little islands off in the distance, more abut the little hut village just beyond the snowy mountains that we see but never interact with. There is nothing in KQ6 that in terms of the lands that really captures and fires the imagination. KQ6 is largely contained in a small environment, and all o the islands are rather small themselves, and travelling back and forth from island to island throughout the game gets repetitive and a bit boring after a while. I like going from Point A to Point B to Point C, not going from Point A to Point C to Point A to Point B to Point C to point A again.
Also, I love the fact that KQ5 is so random. It doesn't take itself too seriously and is enjoyable by both kids and adults alike in this matter. It's incredibly original. I mean what other game has something the character defeating a monster by throwing a pie in it's face? It's just so random that it's brilliant. The game throws everything that's possibly random at you and challenges you again and again.
The lighter moments in KQ6 feel too structured, the puns and whatnot make a little too much sense, it's a little too calculated. I mean you slay the Minotaur by showing him the red scarf...How..um clever? The Hole in the Wall is LITERALLY a living hole in a wall. The Book Worm is LITERALLY a worm who lives in books. It's a little too overwrought and overthought---which is a flaw I find common with a lot of Jane Jensen's games.
Also, I feel in the larger context of the series, KQ6 with it's darkness sticks out like a sore thumb, especially if you take each game at face value. Every KQ game at face value is generally more or less lighthearted, with some serious moments. Every KQ game has an element of surprise and randomness; Random encounters and creatures, whereas in KQ6 it feels all planned out, thought out, and thus a little sterile. KQ6 sticks out with it's political intrigue, murders, and overall VERY serious tone. I mean we go from throwing pies at Yetis in one game...To making Death himself cry in the next. That's a pretty big jump.
It's like one of those old math problems: "Which of these is not like the others?"
A) An evil witch driving around in the batmobile with the batman theme music playing
B) Every character both good and bad showing up at the end, despite whether they're dead or not.
C) Defeating a yeti with a pie and activating a magical machine with Cheese
D) You help out Dwarves by cleaning their house for them and share soup with them and a minstrel plays horrid out of tune songs.
E) Meeting the Lord of the Dead and making him cry.
The light hearted moments in KQ6 end up feeling a little disconcerting as the game breaks it's serious atmosphere by having light hearted moments which are painfully lighthearted, and feel forced; It feels like those light hearted moments were just shoved in there since lightheartedness is expected in a KQ game. It makes the game feel uneven, as if it doesn't know whether it wants to be a dark, serious, mature game...or a family friendly childish game. It feels kind of bipolar in that respect.
Case in point, the Isle of the Dead. You have a creepy, spine tingling realm full of restless spirits, rotting shuffling zombies who are obviously in some cases murder victims, the land you're standing on looks like it's made of flesh and an ominous full moon hangs over the sky. You've got a great, dark, spooky atmosphere worked up here...And it's shattered in one moment by the Dem Bones gag which detracts from the overall seriousness of the scene. It feels like it was thrown in there at the last minute to lighten things up a bit. Like somebody perhaps thought, "You know, this is getting a bit too dark for a KQ game, don't you think we should lighten up a little?"
It and KQ8 are two very big breaks in the formula of the series; KQ6 in tone and writing; KQ8 in tone and gameplay. Even KQ8 for all of it's non-traditional elements retains a fairly simple yet grand plot. KQ6's plot is a little too Byzantine for my tastes.