That's your evil plan? Seriously?
- After he escapes, we see Jarod take on hundreds of new identities and demonstrate the ability to learn just about any skill in record time and insert himself into nearly any social group. The Centre knew about these abilities, which were precisely the reason they took him. So, you have a genius who you know has the ability to be the perfect spy and/or con man... and you decide that the best way to use him is keeping him locked up in a basement, interacting only with your own staff? Sure, they had him running simulations, but compared to what they could have done with him, that's just wasteful.
- If they keep him locked in the basement, they can control him, both physically and emotionally. If he's off on some undercover operation and gets it into his head he's tired of being an agent, he just walks away and they might not even know it for quite some time. By using him to plot out scenarios that they can give to other, field-reliable (and likely expendable) agents, they're making the best use of their prime resource they can without risking losing him. And considering just how long it was until he got it into his head to escape, their plan obviously worked fairly well.
- In addition we see them sell his simulations to clients. They didn't need him out in the field.
- Plus the Centre doesn't have an evil plan. The 'only' want money, the do not care if their simulations are used for good or evil and with Jarod they made quite a lot of money.