Having seen both multiple times (not to mention doing crowd control for Fantasmic numerous times at DHS) I can honestly say the changes and differences are not as substantial as you make them out to be. Grant it, I only worked there in summer of '08 but I saw it enough times to note that, while some areas differed largely in content, the show itself was not that dissimilar.
Let's take a look at some of the core differences:
Run Time: DLR is 21 minutes, DHS is 27 minutes
Seating: DLR forces you to camp out hours before the show. God help you if you're in those areas and DON'T want to see Fantasmic. You'll likely end up watching it in its entirety anyway in a trek as simple as going from Pirates to Haunted Mansion thanks to the obscenely huge crowds.
DHS has an amphitheater that seats approximately 2 - 1.5 hours before showtime. But guess what? I've gone back when they had a nightly schedule and I was almost every time capable of getting front row center seating 45 minutes before showtime despite the fact that the center section looked completely full from the top.
Setting: At DLR it's Tom Sawyer Island. At DHS it's a faux mountain. Um sorry, but the show seems SO out of place on Tom Sawyer Island. It's almost as if they didn't have a good place to put it so they just wedged it in there. The show is much better suited to a custom-designed stage like the one at DHS.
Content Differences: DLR uses a Jungle Book themed sequence with a giant Kaa (snake) followed by a strange Pink Elephants on Parade sequence followed by a Pinocchio sequence which is really just a cardboard cutout moving back and forth. At DHS this segment is replaced by a Lion King segment which segues into a bubble sequence showcasing different Disney films while blending the music together. To be honest neither of these sequences really stuck out to me as very entertaining and screamed filler.
They then do a Peter Pan sequence utilizing the Sailing Ship Columbia. While cool because the ship DOES look like a pirate ship here's the main problem: the ship is constantly in motion during the entire sequence. If you're seated closer to Frontierland, you spend a good five minutes of the sequence staring at the stern of the ship and listening to the soundtrack because its too far away to see what's going on. It's passed you long before anything good has happened. At DHS the Pocahontas segment, although not the best choice, takes place on the main stage, thereby giving all guests a good viewing angle of the entire sequence which I might also add segues MUCH better into the princess sequence than just randomly ending and moving on as DLR's does.
Villains: DLR doesn't overdo it here at least. Keeping it simple with just Snow Queen, Ursula (with the recently added Flotsam and Jetsam floats), Chernabog and Maleficent isn't overly distracting. On the flipside, the Jafar sequence at DHS is cool and the giant snake works better in that scene. DLR wins hands down with the new dragon. I remember seeing Fantasmic for the first time and being so disappointed by that excuse for a dragon. The new one at DLR is much truer to the original advertisements and DHS needs it desperately.
Finale: The Mark Twain at DLR is much better as it's larger and able to hold more characters. The Steamboat Willie replica is too boxy and fake looking. However, on the overall finale, I believe DHS wins and here's why: Mickey emerging from the very top of the mountain gets me EVERY time. Random Mickey on top of some pre-existing cabin? Not so much. Oh wow Mickey, look at you stand on that roof. SO dramatic! Not to mention another key point. Between '07 and '08 DLR dramatically cut the amount of pyro in the finale. DLR has to always be careful about that stuff because of the close proximity of a freeway and houses to the park. So their finale is more 'laser-centric'. DHS on the other hand doesn't have to give a flip about pyro and goes all out, making the finale much more exciting.
So, pretty much they both have their pros and cons but I think despite the recent enhancements that DHS has a version that's still better due to fixes they made to the flow of the show (Pocahontas) as well as aesthetic and comfort (stage, finale, amphitheater) that DLR lacks.