Recs.
Updated
Specs
Pros
Pro The Institute's main concept is not bad
The core philosophy of the Institute is science for the sake of science. The events of Fallout 4 notwithstanding, I am certain that prior to the year 2287, if the Institute wanted to wholesale slaughter the denizens of the Commonwealth, or otherwise take it over, they could have. They certainly have the synths, resources, and intellect to do it. However, the fact that they haven't done this proves that any detrimental effects that the Institute has had on the Commonwealth is not the result of malicious forethought.
Cons
Con Morality
Despite their technological advancements [Refering to their progress in Synth creation and Teleportation Technology] they do not see their Synthetic Humans as living beings and rather as machines - Despite Synth Components being the only technological thing about them. This view can be seen as Morally challenging as they essential keep Synths enslaved. The Institute is also known for kidnapping and replacing people with Synths...even if the victim has children or a spouse.