I think the writers are already heading in this direction but....
It would be cool if the T-1000s chose what side they fight for. With the nature of the 1000 (no moving parts, computer chips, etc) how would Skynet program them. It should be that skynet cant control the 1000s so it discontinued the line, which would also add texture to the TX in T3. Sky net cant control a pure T-1000 so it had to make the chassis more like the 101 with a liquid metal cover.
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