The nipple out off the wall seems to be galvanized - it has got to go. Most likely it's threaded inside the wall to a female elbow fitting.
1. Disconnect the flex supply line from the angle stop to the toilet tank.
2. Using a plumber's wrench, remove the nipple. Having problems? use some force or use a bigger wrench with more torque. Last resort: Cut the wall and assess the situation.
3. Install a new brass nipple, a new 1/4 turn angle stop and a new flex connector. Test for leaks.
1. Disconnect the flex supply line from the angle stop to the toilet tank.
2. Using a plumber's wrench, remove the nipple. Having problems? use some force or use a bigger wrench with more torque. Last resort: Cut the wall and assess the situation.
3. Install a new brass nipple, a new 1/4 turn angle stop and a new flex connector. Test for leaks.