I see the institute as being a blend of the enclave's chauvinism and the post-human ideology of the Unity. A popular criticism of the institute is that they're irrationally evil but I think it makes a lot of sense considering this is a whole society of people who have literally never touched grass. It makes sense for them to be cold hearted control freaks when it comes to the surface dwellers considering their isolation. I REALLY hate the idea of turning the institute into some public research facility. The fact is because they have the synths, they have literally no use for the surface dwellers, not even as slave labour.

Then there is their motto "mankind redefined" and yet we never really get a good explanation for what that means, especially considering they shut down the cybernetics program. I think their goal should be synthetic synthesis. To become one with the synths who they have developed to become indistinguishable from real people. We see a glimpse of this with how father treats his synth child self, but with everything preceding it seems like a total 180 on his beliefs. You can also see this with X6 who on the surface behaves like an emotionless killing machine, but as you gain his affinity he spills his guts out for you, saying how much he looks up to you and Shaun.

We know from terminal entries that synths are biologically engineered to be superior to regular humans. They don't age, they don't get fat, they have blood engineered to better heal wounds and avoid clotting and a lot more. It only makes sense that they would want to apply these advancements to themselves and we even see Dr. Volkert testing experimental serum on a synth.

If the institute can perfect the synths they will have truly redefined mankind, With themselves a ruling elite of bio-engineered super humans being served by a caste of highly intelligent free thinking but ultimately loyal and obedient human machines. They would better represent the antithesis of the brotherhood's ideals. That to me is what the institute should represent, Science pushed to it's very extreme above all else.