Hands down The Unity and the Master.
As awesome as the 'grey morality factor' is, its starting to be a bit cliched.
For me, it was the wealth of information that we can discover about who the master really was and how exactly he came to his current state almost through a day by day view.
The other factions really didn't have much information about them annd already mentioned, were portrayed way too one sided evil.
Instead enclave could have offered a sort of bread and circuses life. So what choice is 'moral', forcefully destory this peaceful life regardless of those who live it in order to justify human choice. They could have also a more sympatheic back story to the legion/enclave also.