My thoughts are to keep it in lockstep with Substitution. Level it to 25, and keep it there until we need to level it with Substitution.
As for Shadow Imitation supposedly being the best, longterm... I don't really see the point. Kei already has a ranged option, and it's pretty powerful when supplemented by our seals (KISS, Explosives, etc) and her ninjuts (CotWG, looking at you). I'm not sure it's worth it to raise Shadow Imitate using Yamanaka XP, given how long it'll take. And her "real" XP is better spent elsewhere, imo.
There has to be something there that we're not able to see yet. Kei, stop being such a square and spill the mechanics. We're missing nin, and thus, not legally people. And that means we're immune to treason accusations!