At the risk of beating a dead horse...Simon's Quest. I loved the game, but it would be cool to see a version that addressed gripes that a lot of people had.
They could change some of the means of progression to be less obtuse (like kneeling at the right place with the right crystal), but still keep them as a decent challenge to solve.
They could definitely rework a lot of the messages the townspeople give you so that they make more sense (although I still like the idea of some of them being liars). Maybe give one or two of the houses some secret monster/cult-like lairs that could work as combat areas, just to add to the sinister feel of the game, and the creepiness of some of the people you interact with, with them being followers of Dracula or something. I dunno, I'm really just spitballing with this one.
Keep the dilapidated look of the mansions, but make the bosses engaging and worthwhile. Every mansion should have its own boss. Maybe scrap Carmilla's Mask entirely and just put a more interesting boss in its place.
Keep Dracula's castle ruins, but make the fight with Dracula more memorable. Revamp his appearance, but his wraith in black look was kind of cool, so still go off of that.