This is going to be a bit of a long winded reply, but i have a very specific hope for the attraction after refurbishment. Of course as ever, this is pure hypothetics, and there'd be no chance it'd ever actually happen, but i'd like to put the idea out there and get some feedback on it.
The blog i linked in my initial post brought up the idea of how the ride is a lot of vignettes without a clear story, and how something that could elevate the ride is playing into more out-there and uncanny visuals. My thought is, in-part based off Kubrick's The Shining. How the Overlook Hotel is a spatial impossibility, and that the initial build up of ghosts is scarier than the ghosts themselves. Both of these apply to Phantom Manor in a big way
For instance, examining the exterior of the Manor and then what we see of it inside, it is impossible. Even the ballroom might be longer than the outside façade itself. If you look at the wealth of concepts that went into creating the original Haunted Mansion in Anaheim, the idea of spatial impossibility was played with. And of course, the Stretching Room is the idea come to life. The dead playing with the physical.
The same can very much be said for the build up to scares. Once again returning to the original Haunted Mansion concepts and the eventual execution, in the attraction yourself there is the threat of the ghosts manifesting, but apart from the Ghost Host, and the hand reaching out of the coffin, you see nothing until the Madam Leota scene, which transitions you into the realm of the spirits manifesting. Of course this isn't applicable to Phantom Manor for story reasons, but to an extent, it adheres to the idea of an unseen threat.
So of course it would be sacrilege to change the ride to any major degree, and the ride simply couldn't majorly play on people's psyche's', but here is my idea for what the Manor could be.
The attraction tells the story of Melanie Ravenswood, the Bride left at the altar, and the evil Phantom who taunts her (who may or may not be her father. Visual cues to hint but people can make up their minds.) Some of the story can be told through narration, but visual storytelling is important, potentially such as the portrait image i linked in an above post. I think the outside queue is incredible as it is. You know something has gone wrong here, and as you wind your way through the gardens towards the house, there's this oncoming feeling of doom. The ride would begin as before, the stretching room with the hanging above clear, and loading through the portrait gallery. Here is where my proposed changes begin: As the ride begins to progress through the house, we get glimpses at Melanie, however this is the only real encounter we have We are aware of the Phantom's presence as our narrator and that he was hanging a man in the stretching room, but other than that taste of his nature, we don't see anymore of him until later. So other than Melanie, we don't directly see any other ghosts, only the threat of them and the Phantom. This is where i make my first major diversion, the Madam Leota scene is replaced with a pitch black room, with an animatronic of the Phantom, still skullfaced, lurking silently in the darkness. The Phantom's evil corrupts the very room around you as he brings forth more spirits from the afterlife to this mock of a party.
The ballroom is utterly perfect, and nothing needs to be changed for it. And i'd say neither does the Bride's boudoir, except some fixing up of the effects. As we leave the manor onto the muddy plane outside *and with the back walls being installed with video effects to simulate rain and wind on the trees*, we pass by the Phantom and his demon dog as he laughs, here we begin to slowly descend into the catacombs. Around us Skeletons emerge from out of their coffins, but this is where things change once again. There is no skeletal Bride, there is no singing busts (as much as it pains me to say so), but there is only the physical dead, emerging, moving towards our Doom Buggies. But we safely turn the corner and leave the caskets. But we are not in Phantom Canyon, and we certainly are not on the surface.
Still underground in ramshackle mine tunnels, we pass through as the ceiling above us quakes, as if an earthquake is occurring (see? plotline lore there), and what becomes immediately visible to us is that we pass by Native American burial plots. THATS RIGHT. The Manor, and the very town of Thunder Mesa was built on a spiritual burial ground, which has caused the curse of the town. For now, the rumbling above has stopped as we slowly cruise past mining equipment and trains that move without an operator, as well as Big Thunder Mountain rockwork allusions and signs saying "Property of the Thunder Mesa Mining Company - by the order of Henry Ravenswood". And then, for one final time, as if the sign was his cue, we come across the puppet master, the Phantom in all his decomposed glory. Laughing at us with his arms maniacally out, standing in a dark cavern ahead of us. We swerve to miss him and the mine surroundings have changed to stone. We're in a cellar. The cellar of Ravenswood Manor, and ahead of us, Melanie, not skeletal, but fully formed, silent and sad, points to the way out, saving us from the Phantom's evil. But the Phantom tries one final time to keep us trapped in his domain by rocking the doom buggy as he appears above it in mirrors we look at, but his grasp loosens, and we depart.
On our way out, instead of a little Leota-Bride, there's merely a portrait of Melanie that's illuminated by some unseen, ghostly light. Then we exit to the outside world, and into Boot Hill, where some good old fashioned grave stone fun is.
Apologies for the long and rambling hypothesis, but this was just my thought. My personal hope for how the attraction could be made even better. I'd love to hear some feedback.... and uh, sorry about clogging up this thread

Have to recommend this blog for its tireless amount of work and effort that goes into all its posts, and offers some incredible information about the attraction's various incarnations:
https://longforgottenhauntedmansion.blogspot.co.uk/