So you've failed once, so you send back your shiniest poly-mimetic alloy terminator, but it fails because the resistance sent back a reprogrammed T-800! You know, or could reason that the T-800 would have to have encountered the targets of the T-1000, and they would have become familiar with each other as they evaded your near perfect killing machine.
Why not send back another with real infiltration programming (the T-800 is supposedly an infiltration unit, no?) so that it spends some time getting Connor to grow familiar with him, fooling him into thinking they are chased and then when he least expects it, the unit turns on him.
Is Skynet not capable of thinking in this out of the box manner? Did it not have enough T-800s to send back? Was it just designed by a physicist, and thus brute-forced every problem?