Actually, it never stated he doesn't take over either. It's a pretty ominous ending.

True, but fans have a tendency to beat certain theories into the ground. "Evil Yes Man" certainly might pop up but it's just as likely that it's not something that's going to happen either.
(I'm sure you'd like it anyway since the most likely "Evil Yes Man" ending would be Mister House having failsafes)
But I'm inclined again to think Obsidian won't deny players their kingdom.
Here's my thoughts on the merits versus downsides of the two.
Pro-NCR+ NCR is an established liberal democracy. Mojave citizens will be given franchise when taken over by NCR.
+ NCR has a standing military that, while overwhelmed in the Mojave, is basically the only organized military left West of the Colorado.
+ It has a thriving economy including beef and caravan trade.
+ NCR has programs for the development of infrastructure and agriculture.
+ NCR seems to support social programs for the poor and relief efforts.
+ Caesar's Legion is a direct threat to the Mojave and one which will require substantive efforts to defeat them. This is still the case even the death of Caesar and Legate Lanius (if so inclined by the PC).
Anti-NCR+ The NCR military is a joke. 3 weeks of training for recruits and effectively the NCR Rangers being badass by on the job training and being a mixture of tough-ass [censored] from the beginning. It's apparently composed of extremely talented veterans with a lot of skill and raw recruits with almost nothing in-between. Without the Courier, NCR gets DECIMATED militarilly by Caesar's Legion.
This doesn't bode well for NCR being able to fulfill its military obligations. If they can't fight the Fiends then how are they going to fight the Legion?
+ NCR doesn't have the necessary manpower to handle garrisoning the entire Mojave Desert, especially not without local support and there seems to be very little of that unless the PCs provide it with the Great Khans and the Enclave and the BOS.
+ Travel times are a [censored] for NCR with no railroad systems in place and no support structure. It's failure with the Powder Gangers also indicates the bureaucracy may not be able to do any of the building that they promised they could do.
+ NCR is going to be suffering a major famine in a decade if the research into plants and agriculture doens't plan out as well as the sharecropping.
+ NCR apparently has more power needs than it does power given it needs Helios One and Hoover Dam.
+ NCR's military is HORRIBLE at peace-keeping if its response is summary execution for any and all crimes.
+ If NCR conquers the Mojave, it's moved its borders directly to Caesar's and will be immediately in a state of war with its border far from its center of power.
+ NCR doesn't protect its caravan structures, instead having privatized concerns handle their security. This means their economic strength can probably be dealt with directly as opposed to through government intermediaries.
Pro-Independence+ The government of New Vegas may be determined by the player.
+ The several hundred Securitrons under the control of Yes Man will provide a military to the Mojave which will be capable of defending it against Caesar's Legion without the likelihood of an NCR withdrawal. Their "base of operations" will also be very close.
+ Encouraging the Khans to leave the Mojave instead of allying with NCR results in the joining of the GK with the FOA, resulting in Wyoming being essentially reclaimed from barbarism.
+ The resources of Hoover Dam and Helios One will be more than sufficient to supply their needs for the centuries to come power-wise, allowing the excess power to be sold to NCR at a cost that can be used to provide money for rebuilding Las Vegas' infrastructure "in-house."
+ The FOA support independence and can be encouraged to become "nation-builders" like they were back in NCR without all the current animosity towards them from the leadership.
+ The Gun Runners and Crimson Caravan show no hesitation in dealing with the independent Mojave if Van Buren is any indication, so trade will continue with or without NCR.
+ Mister House's tribal associates seem perfectly content to continue on underneath you and it is unlikely that there will be much instability with the upgraded Securitrons.
+ Provided you have no problem with eliminating the Van Graffs and have removed Archimedes I and II as options for the Brotherhood, their harassment of travellers regarding super tech won't be a problem since they're only interested in weapon technology.
Provided the Courier is a member of the BOS, they should have no issue with assisting the stabilizing of the region.
+ Representation in the government would be much more localized should the PCs choose to institute a democracy (which, admittedly may make things awkward with the BOS in the future - oh well)
Anti-Independent+ A lack of reinforcing army should Caesar's Legion choose to attack again.
+ The potentiality for NCR reprisals.