NOTE : Liberty prime died during Anchorage and hence should be presumed dead as he doesn't make an appearance in fallout 4 unless the Player gets the agitator for the Brotherhood.
Transportation :
Teleportation is stronger than vertibirds. All the institute needs is one courser cloaked in a stealth boy to infiltrate the BOS facility and spawn 1000s of synths inside it.
Winner : The institute
Weaponry :
The institute weaponry being limited to only institute pistols and rifles is weaker than a wide array of weaponry used by the BOS. Despite having a faster fire rate the institute weapons would have higher difficulties in piercing stronger armor like power armor and heavy combat armir because of the reduced damage.
Winner : BOS
Armory :
Synth armor has better energy resist stats than combat armor. Since most BOS members use laser weapons. Synth armor wins over combat armor. But higher ranking brotherhood members also use power armor which is much stronger than synth armor.
Winner : Tie
Army numbers:
Synths can be produced at a very fast rate. The BOS has certain protocols during recruitment which limits it's no. of recruits.
Winner : Institute
War experience :
The institute being operated by scientists and having coded synths lack war experience unlike the BOS which are fresh in war experience having fought the enclave.
Winner : BOS
Allies :
Both of the factions are highly untrusted by the settllers . Since most of the factions like gunners, super mutants etc. being unaware of the institute's goals see the brotherhood as a single threat. They are likely to support the institute. Settlers being tired of reports suggesting people getting replaced by synths are likely to aid BOS.
The big amount of enemies BOS has which includes The enclave, ferals, gunners, raiders, mutants etc. Exceeds the amount of enemies the institute has.
Winner : The Institute
Morale :
The institute synths being machines have no feelings of pain or remorse. Meanwhile, the BOS can get both encouraged or discouraged based on how a war proceeds.
Winner : Tie
Traitors or defects :
It's very unlikely that people will beyray the BOS. Synth sensors can start malfunctioning.
Winner : BOS
Conclusion :
Despite the institute and BOS both scoring 3 ticks. There are some factors like war experience and transportation which have a greater impact. I am no army personnel, so I can't say for sure which factor matters more. That's for you to decide.
Source: reddit.com
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