Hoo boy, I must have spent so much time thinking of a coherent argument on keeping that list.
Basically, I argued that the Allies list isn't redundant. Even if everything in the Allies list can be found in the "Characters" list, the Allies list serves a more specific function, just as we have boss and enemy lists along with a character and species list.
Wouldn't the "Bosses/Enemies" list be redundant with characters and species, in the same way as the Allies list? Sure, the Allies have a bigger chunk of characters than species compared to the Enemies/Bosses list, but the bulk of the Mario series is defeating many, many enemies, so it's really more of a byproduct than a proportion issue.
The biggest problem is probably the realization on how these lists are formatted, though.
They're incomplete. For instance, playable Super Smash Bros. Brawl characters, especially Link and Kirby, who also play protagonist in the Club Nintendo comics, are not in the Allies list. Koopa Troopas, who are consistently allies in the Mario Party series, are not in the allies list. Shy Guys are in the allies list, but their game is... Super Mario Bros. 2 Mario vs. Konkey Dong.
The debut medium after the character. Good for rarely occurring characters, not so good for the staple characters.
The definition for what is an "enemy". Is it generic mook, a rival, or simply someone that is an obstacle (Glitz Pit Security comes into mind)? Do they have to be sometimes enemies, sometimes neutral, sometimes allies, or do they have to be always enemies? Does Mario qualify as an enemy because he was an antagonist once?
What is an "ally"? Are they the playable characters (like Boo from Mario Party, who is one of the serveral that can save the Star Carnival from Bowser?)
So yeah, questions, questions... maybe we're revealing a flaw in these lists.
My idea is to ditch Allies, Enemies, and Bosses lists and focus on organizing the remaining lists. The list will still be alphabetical, but maybe special characters or other things can indicate who are enemies, who are allies, and who are neither. But that kind of stuff can be messy.