I don't know what ZXNova's saying I wouldn't say no to Inu Sakuya. (although it'd typing would confuse me. beast/steel? beast/reason? beast/ice?) She'd probably get a massive re-stating though compared to whatever she had in the various hacks she appears in.
As for the other puppets, I feel like Lie Meiling's more of a shiny pallet then anything. Maybe she could be like a scripted encounter, a normal Meiling forced shiny with a dark move that Meiling dosen't normally get? the other ideas aren't bad, but if you want a pair suggestion, why not a Mystia/Kyouko puppet? I know there's a sprite for it floating around out there.
Also to bring up something for way earlier, OH HELL NO on the anti-grinding idea elyk mentioned. I know we could use some sort of anti-griding but I don't think it should be THAT extreme. scaling gym leaders based on your own levels would defeat the whole point of engaging in non-important battles IMO. (well, outside of catching more pokemon/removing roadblocks)
I'd say a good way to curb it is to either use B2/W2's EXP system or modify it so that wild pokemon simply give out NO exp if you are a certain level higher then them. (trainer pokemon still give out normal EXP since you can't really "grind" off them, vs. seeker aside) That way you can still "grind" but there's a clear level-limit that can be defined. There will still be overgrinding for the people who like their emulators running at 1000% or don't mind the tedium, but that's unavoidable in any RPG. unless you are paper mario sticker star, and well, look how that turned out.
One last thing is that I personally recommend we go with "puppets" and not "Bonéka" since, to be honest, I kinda have a bias against that word since I mentally associate it with achiya's stuff... not to mention that "puppet/puppets" just sounds a lot smoother to me.