I choose order of chaos, Autumns enclave would have control, eden was just a tool for moral, a symbol. Now useless, then the enclave could rebuild.
You would pick tyranny and fascism over integrity, freedom and human dignity. There track record of slavery, secret experiments, murder and intimidation shows their little better then Caesar's legion. Throw in the attempted genocide and you can easily say Caesar has the moral high ground.
House is like them, order, he dosen't treat everyone nicely, but it is the best thing in the situation.
I don't see Securitrons roaming the wastes attacking random travelers and capturing slaves, but the Enclave certain did that. House has a plan for the future of humanity. The Enclave has an ideology to rebuilding America, the same kind of ideology that led to the great war to begin with.
And that is the key difference, The Enclave wants to rule and control with the pure humanity on top. House could careless about someone being a ghoul, a super-mutants or a talking deathclaw[if the Enclave hadn't exterminated them]
House goes after threats to his plans while the Enclave goes after threats to there ideology.
You cant say a faction is weak when its only weak for game reasons
I can say a faction is weak because they've had there already small numbers devastated twice. They couldn't face the NCR head on in Fallout 2. Why could they suddenly have the strength now when the NCR military is even stronger and there numbers and resources are even less.