The way i see it, yes. That was his plan the whole time. If you go along with his mad scientist bullshit just because he's your son and agree to become the director then you've played right into his hands. You've been brainwashed into following in his footsteps.

He manipulates you from the moment he lets you out of the cryopod. The whole thing was merely an experiment, and should you survive and find him, it's an opportunity to groom a successor. He lies to you, guilt trips you, and pulls the family card the entire time you're together in order to bring you over to his way of thinking so you will carry on after he's gone. And yet he still basically tells you that he doesn't love you or see you as a true father figure.

To the institute you are just Shaun 2.0. A "fresh" mind that they can bring into their fold. One that hasn't grown up seeing the horrors they have perpetrated on the Commonwealth. But you aren't a baby, so a more subtle approach is required rather than just raising you as one of their own. Notice how as director you have no way to influence anything? They convene a meeting to ask you what you would like to do about the BOS, but even if you tell them to avoid conflict they disregard it completely and continue with their plans for war. So what exactly was the point of asking you?

My theory is that all the main staff have a part to play in Father's scheme. Appointing you director is a way to give you the illusion of control but their goal is to slowly assimilate you, while the division heads continue to make the real decisions until such time as you have accepted their ways and can truly assume the position. (Oops, i accidentally made a Fisto joke and ruined my train of thought) Where was i... I guess that's it. Unless there's DLC that allows you to run the place how you see fit like shutting down synth production and actually helping the surface that's my headcanon for the institute ending. And that's why i prefer the BOS. Ad Victoriam motherfuckers.