Getting into specifics, it is believed by many that the "toon_sheik" file is actually in reference to Wind Waker's Tetra, as there's no such thing as Toon Sheik (plus both Tetra and Sheik are Zelda disguises one way or another). It does make sense, as, like Tetra, both Toon Link and Toon Zelda are from said game, but no sources have ever confirmed this. Maybe Toon Sheik was indeed planned as a brand new character, who knows!
In addition, though unconfirmed, it is said that Mewtwo, Roy, and Dixie Kong had the most work done on them, as victory fanfares can be found in the game's files for the former two (including a Wii remote sound for Mewtwo). Dixie Kong had a working prototype at one point and was apparently supposed to have a tag-team mechanic with Diddy Kong (like in Donkey Kong Country 2), but due to complications in programming, she was cut and Diddy was developed as a standalone character instead.
Finally, the assumption of Plusle & Minun being part of the "forbidden seven" stems from a file that actually reads "pra_mai". This filename nearly corresponds to their Japanese names (Purasuru and Mainan), hence why it's thought that Sakurai and co were referring to them. It also makes sense, for the duo are the "Pikachu" line of Gen III, much like Pichu is for Gen II in Melee. The evidence against this however, is that the Ice Climbers and potential Diddy-Dixie combo each has two separate character files - they aren't shared under one file. A possible explanation for this is that the electric pair used a completely new mechanic altogether, keeping them unseparated, unlike the other two duos. Despite this, it's interesting to note that Plusle & Minun, along with Pichu and Mewtwo, are all special criteria Pokémon trophies in Brawl - suggesting that they were bundled together as a group of planned characters.