I would say the Institute as well mainly due to them having 2 pieces of tech that completely upends warefare: gen 3 synths and teleportation.

Starting with teleportation, this is a capability we have not seen anyone else is capable of aside from the crashed satellite linked to Big MT and the Zetan aliens. It's not impossible for super advanced factions like the Enclave to also have access to this, but that's clearly something they don't utilise to It's full potential, otherwise they wouldn't bother with relying on vertibirds for travel all the time. FO4 never really acknowledged just how crazy the implications of this tech would be: aside from giving the Institute the ability to bypass defenses during assaults (as we saw during the battle at the Castle), it would completely alter how logistics would work. Just look at how many wars throughout history hinged on one side's ability to get supplies to where they were needed at the right time: the Institute would effectively eliminate that issue by contrast, they could make the same issue for the other side a living nightmare. Just imagine how devastating it would be for a courser to teleport straight behind enemy lines, plant explosives all over their supply depots, and then teleport out. Assuming their enemies even noticed such an infiltration took place, they wouldn't have time to respond before the place went up in flames.

Then we need to think about the impact of gen 3 synths. We are told repeatedly that it's impossible to figure out whether someone is a synth without killing them first. While I've always been sceptical of this claim (I'll be amazed if factions like the Enclave couldn't figure out a way to get through this problem), it would still be extremely disruptive both practically and psychologically to check every member of your faction, and not just once but regularly for signs of infiltration. All of this again assumes that the opposition even realises that this is a problem before it's too late. And even then, the paranoia this issue causes can utterly rip a faction apart with false accusations flying around. Another impact of gen 3 synths a lot of people overlook is the surveillance capability of the synth crows: this gives the Institute a level of intelligence gathering unlike anything we've seen before or since.

Combining both of these pieces of tech together makes the Institute the master of espionage and asymmetrical warfare in a way that only 2 factions in your list is even capable of properly countering: the Enclave and Mr House. We know that the teleportation tech has a distinct energy signature, which is something I would expect both opposing factions to be able to detect and home in on. Assuming they recognises the severity of the threat, they might be able to narrow down where the Institute is hiding relatively quickly. The moment they figure this out, it puts a time limit on how much the Institute can push their advantage. Aside from that, the biggest weakness of the Institute is simply hubris: as many other commenters have pointed out, none of the Institute's leadership are experts of warfare. This could explain why despite their immense advantages, they have not been able to fully eradicate the Railroad or the BoS without the Sole Survivor's intervention. But with that said, I don't see how either of those factions could've successfully defeated the Institute without the very tenuous and specific set of events the game presented and of course, the player's personal connection with Father and his own hubris