Super introduced more item dependencies for spawning order. This means you get the Peril Ring first as a Blue Ring 0.5 (it was buffed to 2 hearts and should appear either in the Overworld or a lower level dungeon.), the Raft before the Flippers, and you need both the Bow and Arrow to find the Longbow or Silver Arrows. The Crossbow also needs arrows to be found. These cross-item group dependencies did produce some bugs, as those who played the first beta of Outlands may recall. Super even had a rare bug for a long time if you found bow, arrow, and crossbow locations in a specific order (fixed in 1.1 and BS).
Super also changed the secret expansion rooms in dungeons into 10 rupee rooms, since even with the dark room hints those were kinda hard to find. Some of those rooms still exist in Alpha, but the DMaps are arranged differently to use the 16x8 maps more efficiently, so some secret rupee rooms got cut. Though the final version of Alpha does include a different kind of secret.
I might have mentioned it before, but all the new dungeons sets are of my creation. 4th and 5th are obviously the entries from those competitions. Ex1st and Ex2nd were made as pseudo 3rd quests after looking at the unpassworded 3rd quest and getting ideas (there is a reason Ex1st has so many traps, that was the first one made). Both of those sets existed as standalone quests on Armageddon Games at some point. As a result, most of the dungeon design was balanced around getting items in a certain order. Notice how it takes until Ex1st level 5 before the ladder is required, and you can get to the item room without the ladder.
For those curious, the ladder was the item in Ex1st level 5, Ex2nd level 3, 4th level 3, and 5th level 4.
Also, Super has two other changes.
If a dungeon room was a more bombs location, the room will now contain an expansion-type item (instead of any item). This fixes certain dungeons spawning too many useful items (like 2nd quest levels 4 and 
. Later randomizers keep this logic, but sometimes there are more expansion locations than expansions, so a normal item could appear in one of them.
If a room spawns a random item when all the enemies are killed, that was where you would find a boomerang. All the boomerangs will now only appear in one of these locations. Note there are more locations than boomerangs, so those well tucked away locations in Ex1st level 7, Ex2nd level 7, or 4th level 7 may or may not end up being your last boomerang upgrade.
Finally, it isn't until Outlands where the Blue Ring and Peril Ring always appear early on. Eppy ran into this issue in both his Super and BS runs (especially the latter).
