Something to remember is that the academy is more of Mrs Powell's pet project. Its not necessarily about making a superhero team, but a place where people with powers might be able to learn some control over them. We can see this with the MC, Mrs Powell figured out that his powers would take time to replicate the powers of others, and those who had a greater degree of control would transfer faster than others. Its why Mrs Powell was always knocking the MC down during exercise and helping him up, as well as other touches like fixing his collar, she was microdosing him. While Riley didn't know, she was effectively doing the same, massages and kisses and sex. But its also why he's having trouble replicating Valentina and Chrys' powers.
Actually now that I've said it, I've just realised Mrs Powell wasn't making a place to help develop a superhero team, she was making a place to create a single superhero. And with the way Shiro has been acting, I'm starting to suspect Mrs Powell has known about the MC for a long time, not his powers but that he's Harsh-Light's grandson. And Shiro is pissed that Powell didn't tell him about MC's grandfather. Because then he'd have a target for revenge.
Based on the conversations in the last couple of updates, it seems to me that Mrs Powell had quite a lot of objectives with all of this. In the newest Harper-scene she talks about her fear that Mrs P. didn't want her in action because of what Mrs. P would do if they ever found Harshlight. I really liked that conversation and MC handled it perfectly, but i suspect that partially Mrs Powell just didn't want to risk her daughter getting killed in action. So just as the Iron Shogun built a tower and locked himself and his daughter inside, the Queen started an Academy for the same reason, but with a bit softer execution. Old friends had similar trains of thought.
Credit to Solace in all this: he was smart about the way he wrote things, because we know some things Queen knew (like how MC's power works), but there is quite a lot of room for speculation and guessing on some other subjects.
For example i don't think that Mrs Powell knew that MC was Harshlight's grandson, but there are still several possibilities:
1. She suspected that MC is related to Harshlight, in which case it's best to keep the boy around to keep and eye on things.
2. MC absorbed Harshlight's power quickly, and so he met him in the last few days at most, which is the best clue she had for a decade now.
3. MC absorbed Harshlight's power over time, which would mean that they are in contact and that can be investigated.
But the best part is that in the end the smart conclusion is the same in every scenario: If even the Queen thought about using MC to find or kill Harshlight then Shiro would absolutely do so too and regardless of anything else, that would put MC's life at risk (either by Shiro or Harshlight). She had to take MC with her and figure the rest of it out later.