I've got a bike equipped with Sora 3300 3x9 levers and Tektro CR-720 cantilever brakes. Braking on that bike is excellent. Your Sora 3500 levers have a slightly different cable pull ratio, but that should be easy to accommodate by adjusting the brakes' straddle cable length.

Switching to Shimano STI levers from Tektro levers, there's an ergonomic difference that could contribute to your braking perception: Shimano STI brake lever pivot points are lower than many other levers. That difference took some getting used to for me since I was accustomed to Campagnolo ErgoPower and Tektro levers.