I have a wacky solution. Most will disagree, but I had the same trouble. I decided to commit to learning claw grip to be faster and have more control. People said it hurts more, but I wasn't able to find a lot of information about it and I feel like people don't do it right. When you play standard grip, you have to rush your thumb from button to button. You can often develop a rolling motion of the wrist and it's just rough on the thumb. With claw grip (thumb for C-stick and B, index on y, middle on Z, ring on R), you just gently press the button you want. You have to find a comfortable position. It will feel weird at first and may hurt. You have to commit, eventually it becomes natural and you'll find the most comfortable position. Even when I do ridiculous shine tech, my hand never hurts. It's just like I am gently typing. No matter your character, claw grip is also objectively faster and gives you a larger range of control.
But just in general, don't play so much, bro. REST. Don't play for thirty minutes to an hour straight. Stand up. Stretch your hands. Put 'em under warm running water. Take it EZ.