I wasted my evening tonight watching a two hour video on why Rebecca Sugar sucks. Honestly, she would be a good Bethesda writer for Fallout because of her mannerisms in storytelling.
Anyway, the real purpose of the Institute was... I dunno. In most of the earlier games, you saw obvious villains and you were able to figure out their motivations early on (Fallout 2 did this really well with not just the introduction video, but also the first time you run into Horrigan where he brutally murders a family of farmers and then brushes you off as you are still a nobody in the Wasteland). Even Caesar's Legion actually pulled this off (very clumsily, but...) because "slavers!"
What did the Institute do? Replace people with robots... have robots wander around, shooting anything... and are basically eggheads who sit around and rant about how the dirt sniffers on the surface need to be eliminated due to impurities (Which, ironically, was also the Enclave's mission in 2 and 3).
If you side with the Institute, you basically would tell the Commonwealth to fear the eggheads and their robots, while it's more interesting to leave the C.I.T. as a smoldering wreckage.