Also, I need to consider wether I want to go on a genocidal rampage on the Institute or not. Considering that the tunnelling Faceless in the University’s West Wing attacked me on sight it seems like I might have issues with them. I did talk to Six before reloading and it seems like the only other people I’ll meet down there will be that Monsignore I kept hearing about, so better to keep one faction friendly.
I never could bring myself to kill anyone in the institute. Sure the higher ups are a bunch of freaks, but i could never ever kill my bro Georgis. He's apex.
Honestly, it's not really that the higher ups are really genetic freaks either. Only Eidein himself is hinted at being some sort of monstrous presence beneath his mask. The rest of them are humans. Mengele-like in some ways? Absolutely.
In fact, they very much make me think what BioCorp was like at the end in some levels, but without the religious fundamentalism. Experimenting constantly, creating new and horrible things, but with a clouded end-goal.
Was it really the institute's mission to take back the surface? Or was it just to feed Tchort? You could question the high level scientists beneath the Apex Technocrats experimenting with the mutagen compound in the same way. What was the end goal of their work? Really, it seems like it was change for the sake of change, experimentation just for its own sake. Yes, from that sort of work we can gain tremendous understandings, but we can also really do terrible things and can risk even losing sight of whatever goals we might have.
In a lot of ways, the work done by Dyson and others was vastly different to those of the mutagen scientists. Successes of the mutagen outcome were too random, or too unique to duplicate effectively (Anton 'Wight' Matveev, Wyatt Pear, Kirill 'Vovin' Gavrilyuk as examples). Two of those successes were, at the least, crafted genome by genome by Dr. Slavkovic himself, a giant amongst giants in the realm of genetics.
Dyson (the Dude) was more interested in a combination of cryogenics and psionics, as evidenced by Slavkovic's own state when discovered as Vitek in-game.