I think its difficult to decide what would be the 'main' ending Obsidian had in mind as it depends on any game they would bring out after it.
I myself would like a mix between the NCR and Independent endings.
NCR takes control of most of the Mojave, including Hoover Dam, but fails in taking control of New Vegas and its resources and technology.
Yes Man takes over from Mr House but keeps up the pretense that it is Mr House, and perhaps tries to put some caps back into the Mojave and NCR instead of being a financial drain.
Caesar or his Legate are killed and the Legion is forced to retreat Eastwards, eventually crossing the radioactive no mans lands and entering what is left of Texas, and attacking and destroying most of whatever has built up there.
When the NCR enters Arizona they discover the Legion has been practicing a scorched Earth policy, trying to destroy as much resources and settlements as possible and leaving the former state half empty of people (most have been taken along as slaves), forcing the NCR to slow down their expansion as they need to rebuild infrastructures.
The Great Khans break their treaty with the Legion but head to Wyoming where they establish an empire of their own (perhaps with help from some Followers of the Apocalypse, to help out the region, and to prevent the rise of a Legion like organization).
The Khans are honorable for the most part but hold on to some of their traditions while having progress and change in other parts
The King and Freeside maintain their independence but become a political power of their own in time.
The Kings help the Followers by trying to keep the number of drug users and alcoholics in check, allowing the Followers' outpost in Freeside to survive.
Most of the Powder Gangsters in Nevada are eliminated, with survivors either joining the Khans or heading East into Nevada to fill in the gap of raiders there, continuing to harass the expanding NCR by destroying caravans and newly built railways.
Goodsprings, Primm and Novac do reasonably well despite NCR taxes.
Prime becomes an important trading post, and Goodsprings a stop over between New Vegas, Primm and California.
Not having been able to take over New Vegas NCR instead establishes a settlement around the Hoover Dam (perhaps with part of it built on top of the ruins of Boulder City) which serves as their capitol in the region and the gate into the East.
The Mojave Brotherhood of Steel survives thanks to the diplomatic actions of the Courier, and make a little progress since the peace treaty with the NCR but they continue to fail to restore their strength and glory.
In time some BOS members head East to search for new resources and technology to claim before the NCR does, still believing that that is the only way to rebuild the organization.
The Brotherhood back in the West continues with their War against the NCR until attrition forces the Elders to sign a seize fire and peace treaty with the NCR government.
The NCR makes big demands of the Brotherhood and pretty much isolates them at Lost Hills by establishing camps around its territory.
Brotherhood members start to leave to build up a new life outside the BOS, some even join the NCR but hide their BOS background.
Elders continue to argue amongst each other were they went wrong.
Jacobstown continues to increase as Super Mutants and Nightkin find their way there, though some groups of Super Mutants and Nightkin who remain addicted to Stealthboy use never join up and continue causing trouble in the wasteland.
Camp Searchlight is never reclaimed and remains a dangerous place filled with mutant creatures and lingering radiation.
Qualified OSI scientists eventually figure out the existence of ARCHIMEDES II and how to activate it. (much to the horror of the Followers of the Apocalypse if they knew)
Kimball and the NCR government decide to keep its existence a secret from the public, seeing it as a tool to be used against the Legion or the Brotherhood of Steel should they start their war against the NCR again.
to join NCR were Freeside and Novac hardly an obstacle for domination of the Mojave. NCR wud not allow such resource drain as Strip to be uncontrolled. As to Khans weren't they just raider scum in F01 and F02? Since I installed NCR mod allowing me to join NCR fraction and military they're as dead as those one in prequel, and I say good riddance. 
Talk to Sargent Bitterroot about their "savage nobleness". BTW Isn't ironic that good FOA ending is as bugged as in FO1. 
Those guys really are out of luck. BOS wud propably survive since they're iconic for entire Fallout setting and they can join their MW or Texan brethren.
