That doesn't seem like the NCR is particularly aggressive to me.
They're dealings in Fallout 2 were more subtle.
They were making deals with the Bishops, a Reno crime family, which would eventually not only bring Reno into the NCR (with a position of power for Mr Bishop), but also used him to force Vault City into joining (through faux raider attacks and internal politicking).
Every city in Fallout 1 has become part of NCR in Fallout 2, and by the time of New Vegas every city that was in Fallout 2 is now a part of NCR.
There is a case to be made for the Shi, though. Their are given to be culturally quite different as to be alien to the NCR, a touch xenophobic and isolationist with quite a bit of self-sufficiency.
There is no word of it, but if any of them remained independent it would be them.
Manifest Destiny is the belief that a group of people have (in this case NCR) that they are destined to expand their country from one coastline to the other. IMO the NCR as a whole believe that they should be the one and only country on the continent. This is supported by their rapid expansion and their persistence to get foothold in any civilized area they find.
I'd actually think that they believe their manifest destiny is to spread democratic civilization to the wasteland. It would be interesting to see if they would indeed annex a democratic civilization they would not have a beef with, somewhere along their path of expansion or whether they would acknowledge them.