^ eh, I must mildly disagree here. There is the whole Yuzu x Julia setup in Arc-V which happened before the series dove head-first into a fractal of self-sabotage. Reminder: Katsumi Ono was simultaneously working on Symphogay during that time, and Fujiaki Asari wrote on Citrus, Madoka Magica and Valkyrie Drive. That was pretty gay given how subdued even het romance is in that shonen-shaped game commercial. (I'd argue probably even gayer than Jaden x Jessie.) There was hope, before it became an incoherent mess.
As for the game itself: there is a time around the release of Traptrix when Konami glanced at Vanguard, Force of Will, WiXoss, and so on, noticed "Waifus = Money" and started churning out female-only and moé archetypes. Those naturally lend themselves to shipping, yet only after the unprecedented success of Sky Striker did they begin adding more yuri undertones (Mayakashi/Shiranui, Live/Evil Twin, Exosister, Labrynth, Mikanko, et cetera).