The Shinkiro is the mech with the most powerful defence systems in the entire series. I want it to be able to regenerate creatures because of how Lelouch uses it to defend Tianzi and others. That puts it in green or black. I also thought this was a rare occasion when hexproof is justified, which puts it in green. By the time the Shinkiro is developed the factions in the series have shifted enough that it's hard to say which colour flavour-wise it should be in, so I'll let mechanics guide me here.

I could alternatively put it in blue, keep the hexproof, and replace regeneration with flickering or toughness-pump.

I'm wanting to focus the colours a bit more, and blue is the colour most focused on technology development. The (Blue-black archetype) wants some defensive knightmares, so even though this is rare, I think it'd fit better in blue than in green.