The 1st time I never saw an Enclave soldier until after they killed Dad and never fought one until I was escaping Raven Rock. This time through I had an Enclave soldier attack me when I was only at level 3 and only been playing a couple of hours. He was just in the middle of the Wasteland and fired at me. And I just had my 2nd Enclave encounter and I'm level 6.
And last time I ran into Brotherhood Outcast everywhere, this time, none at all.
Also the 1st time I played I never saw any ants until I went to Grayditch. This time the first thing I ran into when getting out of the Vault was an ant. I also just went to an area where I thought I would run into my 1st Deathclaw encounter, and instead I ran into a bunch of ants, nowhere near Grayditch.
So, what differences have you seen playing through 2nd or 3rd time?