AZM Ally Shin found a clip of Raph using the sai as they were intended and sent it my way along with this:
I just had to say something about Raphael never using sai correctly and I agree completely. The TMNT influenced my little nerd brain so much that as I got older I forced myself to learn how to properly use a katana, beat myself stupid with nunchaku until I could get form and technique correct, worked with a wonky bo staff and finally got to my favorite turtle and started learning to use sai. And it was boring. As. Shit. Nowhere near as much fun as the way Raph uses them and even attempting to use them that way is so…artificial and impractical when being a sneaky ninja. However, I was completely impressed by the 2007 movie for a multitude of reasons, but none moreso than when the whole sibling rivalry of Leo and Raph came to a head and they finally got all that anger out on each other. And the best part, Raph uses a different weapon before switching to his classic sai and actually relegates them to defense while he uses hand-to-hand to fight Leo. So he does, in fact, actually learn to use the sai correctly!
I’d be willing to give the Bay produced TMNT flick a pass on the origin change if there is some semblance of proper weapon usage. To me, that’d be an worthwhile update.