Why are extra characters still $3?

[Dhalmel]

Probably because they are expecting most players to use their retainers as their Mules and any additional characters as actual PCs as I do.

This is the reason right here. Retainers don't take as much data as a full character does and Square doesn't want to run into the population problem XI had with people having too many inactive characters/mules.

[Betelgeuzah]

This is the reason right here. Retainers don't take as much data as a full character does and Square doesn't want to run into the population problem XI had with people having too many inactive characters/mules.

lol

Square wants more money. Offering a vanity service for unreasonable cost is what brings them said money.

20 bucks for a shiny pony in WoW.
5 bucks for two alternate character costumes in SFIV.
Team Fortress 2 hats.
Overpriced weapon packs in any generic FPS.

SE does what everyone else does. It's not reasonable but it's not mandatory either. Also, it has nothing to do with game balance or whatever, lol. That's just being an apologist.