Disneyland's Splash had a larger quantity of animatronics due to receiving all of the original America Sings figures, while WDW didn't get copies of every single one (Tokyo ended up getting a couple extras that WDW never got, but still not as many as DL). Their Riverboat was also larger.
That said, WDW's Splash had significantly higher quality scenery. Both inside and out. There's just a lot more detail to everything at WDW. It's easier to see the signs of where they were running low on money at DL. They also changed the setting to take place in a sunny hilly countryside with farmland instead of a dark bayou. This is most noticeable the the overhead foliage, reduced amount of water flooding the rooms and the background detail added to the walls. I posted these shots over in the other thread, and I think they serve as a good comparison for the environmental differences-
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In addition, as you also may be able to see from the two images above, WDW received superior animatronics for the main trio of Brer characters. They have better movement but their skins also look better and more closely resemble what they looked like in the film.