But female mobians used to be bottomless back then, it's just after "Genesis Wave" re-design, someone at SEGA mandates no female character is bottomless anymore.
Story-wise there are no explanation why that's happened, why they suddenly went for comfort or protection after fine with nothing for years before.
Ah but Archie comics were not canon to the games. Fiona Fox and Julie-Su were not canon.
If anything, the Super Genesis Wave was more of a attempt to comply the comics to games standards, and that include giving Sally clothes.
Now we have IDW Sonic comics and agan, none of the girl mobians wear any less than the boys do.
Sonic Superstars Officially Takes Place Before Sonic Adventure
Article : https://www.thegamer.com/sonic-timeline-superstars-takes-place-after-mania-before-adventure/
I like to believe Sonic Pocket Adventure was the game when Sonic and Dr. Eggman transitioned from their classic to modern appearances.
The game still played like a classic game and Sonic looked like Classic Sonic despite Modern Sonic in the title. While Dr. Eggman looked like his classic self there was a moment when he tries on his new uniform.