If the Big MT fell flat on its ass I would criticize it just as much as the Institute. However, as it stands now, the Big MT makes sense, and all their insane experiments make sense because they themselves are completely insane and don't even realize there's a world outside the Big MT thanks to them being reprogrammed.
The problem with the Institute doesn't have to do with them not being fleshed out enough. It has to do with what's already there. the fact that they made Super Mutants for 10 years despite knowing that Super Mutants do not help society or contribute to science in any way, and yet the only explanation we get is "Father wills it" on a holotape by one of the scientists down there. The fact they're making all these synths with emotions and feelings and memories and yet despite the Institute seeing the emotions and feeling as a glitch, they don't bother to correct the problem. They just keep pumping out Gen 3s like it's Santa's Workshop on Christmas Eve. There's also the fact they have teleportation built into all their Synth Coursers, yet they can't just put teleporters in the other Gen 3 Synths, so whenever one runs away, boom, they can just pop them back into the Institute for reprogramming? None of that is ever explained. Not even a little.
Super Mutants and Ghouls aren't that realistic, no, but at least their origins, where they came from, what caused them to be made, and so forth and so on all make sense and are at least partially if not fully explained to give a satisfying answer we can accept. In Fallout 4 there's none of that. Nothing is ever explained and we're supposed to just take it all at face value it seems. If Fallout 4 had been set before the other games, say 30 years after the war, and they got rid of the Gen 3 synths, that would clear up a lot of the plot holes right there. But as it stands, the story and plot devices they use make no sense if you've played any other Fallout game, including Fallout 3.
Are the games allowed to be silly and nonsensical? Of course they are, but it should be relegated to a noncanon source and not fuck with existing lore. Compare anything from the Wild Wasteland perk in New Vegas and then compare it to Cabot House or Kid In The Fridge and you can see where the problems lie.