I'm probably alone in thinkin this, but I reckon Shujinko'd maked a pretty good sub-boss. Here's the scenario (say Scorpion did Onaga in):

Shujinko is shunned by his fellow Earthrealm-ers ("None of this woulda happened if it weren't for you!"). Pissed off, and ashamed, he becomes a crazy recluse for a while. He then hears of the "new threat" to Earthrealm. He then has a bit of a "renewed vigour" moment, and vows to take out this new threat himself... Even if it means destroying any of Earthrealm's other hopes.

He's a great candidate, cos he knows every kombat style, and has many special powers. His "destined battle" could be Raiden, who still has it in for him after the Deception fracas.

you are totally correct, i like the bad cop thing i guess that is what you could call it. shujinko should be like the hero who says "I will destroy the threat for my redemption, but if someone else does it first, i will still be the village dumba** who nearly destroyed the realms, so i must destroy them before they destroy the new threat, before i destroy the new threat!!!!!!!" (confusing isn't it?)