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If you don't want him as the big bad of the first movie just allude to him as the guy calling the shots in NYC and the main villain of the first movie just answers to him. Or was just funded by the Foot.
2nd movie is a toss up on whether you want the Turtles to face Shredder and lose or Win? I'd say lose and the separation of Splinter can set up the space arcs while the Turtles spend some time in Northampton before returning to NY to defeat him.
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