Before the revamp with Project New Leaf, there was a separate dialog system that animated character by character. This can be re-enabled by editing the feature AniKeyTextV2 in the client. However, it is highly recommended that you do not tamper with this section of the client when playing on live official servers as doing so can get you banned - RIGHTFULLY SO.
Before the rewrite, Bella Vidrem had an identical twin sister called Elmin Vidrem. While she isn't in the current lore, her portrait can be seen in the dungeon Ludible Time Hall.
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In older versions of the game, furniture in your house could be used to store items that aren't being used (like hats, tops, botttoms, gloves, shoes or mantles). These were called 'banks' and were located under the Storage category of the Home UI. It is possible to re-enable this by changing the FurnitureBanks property to true. However, unused furniture isn't shown in the bank anymore.
The B1 and B4 abandoned mines used to be a good source of resources for high-end gear. Getting them involved getting rusted keys from chests and then analyzing them on Archaeologist Natalie for a price that increased with each analyze. This got axed in the revamp with Project New Leaf.
In the pre-rewrite lore, Dark Lord's real name was Winn Stilton. This was heavily implied in the quest Shadow Seed and accidentally confirmed with the Maplestory 2 Archive release, which included a version of his portrait showing him without his mask. This was a clear homage to Von Leon from Maplestory 1.