i have found three (3) pre-Madoka magical girl games. one of them is a Sailor Moon licensed game from the BESM people. one of them is a Precure fangame currently unavailable in english, and one of them is Princess: The Hopeful. and apparently that one is like four games now but that's a sidetrack.
This does help a few things make more sense I guess. Madoka gets game design brains sparking, there's virtually no other mahou variants to compete with, so dark mahou gets the most exploration and design tech.
you are not immune to Madoka
Majoko: The Dreaming (or maybe Majoko: The Misting, there's a couple different names here) gets a site in 1999. actual system text eludes me, but, there's a character sheet, apparently.
HeartQuest: A FUDGE-based shoujo manga system from 2002. best I can tell, mahous are included in the base system intent, and then get a dedicated module or splat in 2005. there's also a mecha splat for escaflowne i think but uhhhh that's for later i guess
Magical World: Can't find a firm timeframe on this one, but it's in 1.2 by 2005. A setting for BESM and Thrash, not a system in itself, but I'm putting it in here anyway
Tokyo Heroes is published (online, for free) in 2006: It's not just a magical girl game, it's also a super sentai game, but it's very clear about the magical girl influence and its intention to include Sailor Moon in its sphere of design.
FUTHERMORE
Most of these have at least some involvement from Ewen Cluney, who would eventually write the much better-known Magical Fury and Magical Burst. guy knows what genre he likes, good for him.