What I think the core problem that fans and critics alike are really hitting upon is this.

Old school imagineering would have designed the line to be a believable facsimile of an actual grave yard not a graveyard themed line.

So not to be the kind of guy to just shoot my mouth off with nothing to show for it I drew up a small redesign based on the layout of the line,current space available, and what's already there. Granted I’ve never had the privilege of seeing the thing in person so if there are few small inconsistency’s just chalk them up to playful spirits.

Step one the audio fixes:

Change the music in the composers tomb to sound as if it's coming from inside the tomb and cut the volume by about 25%. Ideally I'd want it to only work if you put your ear up to it but beggars can't be choosers.

Rerecord the poet characters dialog. Currently she sounds like a condescending host on a children's TV show. I'd prefer something a more frustrated a tired. After all the epitaph states that she has writers block so In addition to a new voice she should never actually find the rhyme she trying to think of but the rhyme should still be an obvious one.

Change the captains tomb audio to sound as it's coming from inside. Replace the humming with a sample of the wind audio from inside the ride and the far off thunder of a storm at sea, remove the sneezing audio and add some watery tank type noises that sound eerily like something is moving inside it.

Step two the cosmetic changes

First thing first. You have to re-theme the aria just a bit. I was thinking something like this...

Most grave yards are not paved completely so some of the pavement would be re-themed as a dirt path and there are more plants and grass throughout and I changed the switch backs in the line to feel less line-ish. I've separated the guest from the who dun-it statues. The reason is mainly because they're too assessable to the guest and every picture I've seen of them has someone picking a nose or placing a arm around them. This is the best example of allowing the guest to break the believability of the line.

Would you do that in a real grave yard? Probably not. That is why they are now in a planter. I've also rearranged the tombstones and they now have just enough space to feel like someone is buried there (about 4 – 5 feet people were a bit shorter in the 1800's)

I didn’t draw it but the composers tomb would get a repaint to make the metal work above the organ all look like weathered bronze.

Finally here's an overlay of the two versions of the line Mine and the current one, the blue represents the waking space and the orange represents the only space lost to the re-theming

That's how I'd go about fixing it.