One of many reasons my Director is taking a good long hard look at the Gen-3 program to see if its too much of a security risk to continue.
I mean really, the Gen-2 synths are just about all you really need. Aside from blending in, they can do everything a Gen-3 can do. And none of them show any signs of free-thought (with the exception of Nick, who was an advanced almost-gen-3-prototype).
Well you'll find plenty of people on here who view the Gen-3's as 'talkie toasters' and so that's a point of contention IMO. The Brotherhood wishes to exterminate this same race, which to me, if objection is raised to enslaving them, then objection should also be raised to purging them with extreme prejudice.
But I still find the Enclave at least as, if not more 'morally' evil than The Institute if we're talking an objective scale. Partly because, they never planned world-wide pest-control like Richardson or ran genetic compliance checkpoints to purposefully exterminate wastelanders. And it seems like most people in The Institute are unaware of things like the FEV program (which Father purposefully kept hidden from everyone who wasn't associated with the project). I'm not trying to white-wash them, mind you. I just find The Institute's brand of 'evil' to be a bit less maligned. Keeping in mind of course, I supported The Enclave in Fallout 3 too (although I think Richardson was off his rocker).
Although granted, that could very well just be because its easier to emphasize with The Institute since, unlike The Enclave, they aren't treated as mindless clones that purely exist as something fun to shoot. We can *gasp* actually talk to them and hear their thoughts.