Try this, take your sonic game and patch it with the GetExtTypePatcher from FIX94's Github here
https://github.com/FIX94/GetExtTypePatcher
I'm not sure if you know how to use wit or not, but you need to extract the sonic colors game with wit and get the main.dol file from it, and drag and drop it into the GetExtTypePatcher.exe and then repack the iso. then add this line to your script bat file
I'm not sure if it will work or not but it is worth a shot.
Maybe in the future we'll get this as an option with the injection script, with a prompt like "Do you want use WIT (for older Wii titles classic controller compatibility)?".
Thanks again KhaderWelaye!