I can make a few assumptions based on the "phenomenal athlete" and Flight 1 quote. Assuming 7 years started at age 5 to 6, that puts the kid somewhere around 12 to 13 years old. What we generally see from Flight 1 at the uLittle and youngers ages is the phenomenal athlete is put into a forward/striker role and asked to do very little thinking by well intentioned but, nonetheless, idiot coaches that put winning over development. The parents are also major problems because at the Flight 1 level, it is all about winning, winning and more winning.
The fast athletic kid isn't asked to spend time at the midfield, or outside back or other positions. He becomes a 1-Trick pony that uses his athleticism and speed to beat defenders or act as the sweeper, chooses to attack pressure instead of passing around it. As he gets older he begins to identify with that 1 position (usually striker) and is judged by how many goals scored, which is often reinforced by well meaning parents and coaches that are under pressure to win by those same parents.
I don't know if this is your situation, but generally speaking the kids with higher Soccer IQ understand angles, spacing, possession, timing of runs, they know when to delay and wait for help, box in opponents, have crosses like demons and are unselfish players. They play all the positions, even goalkeeper at the uLittle stage. If your kid hasn't been playing all the positions, then his soccer IQ will remain stunted.
Years ago when I was taking my E-License course, the instructor relayed the following story. He was coaching a club team and had a great forward (let's call her Jenny). New season came along and he got two faster and better forwards/strikers. He moved Jenny to the outside back. Jenny was in tears and her parents confronted the coach threatening to move Jenny to another team because she was a "Striker." He met with Jenny and her parents and told them his plan for Jenny. He said "Look here parents, Jenny is good, but she isn't a complete player and growing and if she is going to play at the next level (College) she needs to become a well rounded soccer player. She need to understand all the positions. When a College coach asks here what position she plays, she needs to answer "Whatever position you need me to play." Right now, she only understands striker. We still have a few years to develop her into a complete soccer player. I'm going to have her play in the back and when she has mastered that she is going to be moved to mid. Years later Jenny came back and thanked her coach after returning from her first season playing college soccer.
What should you do? Simple. Sit down with the coach and ask him three questions: (1) what, in the coaches judgement, does your player lack in Soccer IQ; (2) what is the coaches plan to address those deficiencies; and (3) what support does the coach need from the parents and the players to help address any deficiencies.
If the answer isn't sufficient, consider moving your player to a developmental team where the coaching staff puts development over winning (maybe Flight 2 / Silver)