Her programmed intelligence and familiarity with the Darkhold combined with a human brain could mean big trouble for Coulson and the rest of the agents of S.H.I.E.L.D. There’s a reason why the Sokovia Accords of Captain America: Civil War evidently created regulations for artificial intelligence, and the good guys of S.H.I.E.L.D. may discover too late that they made a big mistake in allowing AIDA to assist on covert and all-important missions like the one coming up in the midseason finale.
The episode didn’t explain why AIDA was creating the brain, but the odds are pretty good that she was designing it for herself.
She’d be more vulnerable with a human brain, but she’d also have free will.