After such a great game in SQ4, how'd things get so bad? I guess that one Andromeda guy really was central to the success of SQ....
You do realize that Mark Crowe worked on SQV as an employee of Dynamix, while Scott Murphy took the helm of SQ6 after Josh Mandel... so "that one Andromeda guy" definitely worked on at least one of the ones you hate.
I think it's important to consider more than just the basic stories of the later Space Quest games. As I said in the "best Sierra game" thread of KQVI, I developed a much deeper appreciation for SQV as I spent more time looking for interesting things to do outside of the game's main story. Mostly subtle things, like looking at the ships in the Starcon Academy's docking bay - did you know that if you look at Beatrice's ship before meeting her, and then again after meeting her, you get different messages to reflect how Roger remembers her? Granted, IV had a lot of that too, and I didn't care much for it until, again, I did the Let's Play of it and explored some of the amusing options available. I think if the entirety of SQ6 had as many amusing asides as the Deepship 86 has, it would be among the best instead of the worst. (Seriously, try using the Mouth cursor on everything in the Deepship. EVERYTHING. It's worth it.)
I'd be pretty hard-pressed to choose a single game as my least favorite, but the original King's Quest II likely qualifies. It did away with almost everything that made the first game good and centered around even more arbitrary puzzles, even more linearity, and even more hoping to bump into characters who randomly appear without bumping into others. Letting you retrieve stolen treasures was pretty nice, though. (Has anyone but me gone through the original King's Quest and gotten the shield first? It really works!)
EDIT: Actually, one game I developed LESS appreciation for as I LPed it was Torin's Passage. It's got some great stuff, but the bad parts are absolutely atrocious, and from reading the design documents, it was planned to be that way, rather than trimmed down from something that was going to be much better!