So at the start of the game I saw the NCR wasn't very nice in how it treated the citizens and forcefully claimed territory, so set about defending the citizens and making NCR an enemy, but later I realised they were indeed the faction I wish to support, so I spent the remainder of the game gaining their acceptance and encouraging all other factions to accept the peaceful outcome and assist the NCR in defending against the Legion. In that regard I had NCR, BOS, Khans, Enclave and Boomers all working together at the Dam.

Unfortunately, later, when the plan was revealed, I realised House wanted to fight against NCR, so I decided to help Yes Man and NCR by removing House from power. Yes Man promised that I would have control of the Robot army. This to me made sense, as I would be able to assist the NCR with this army, similar to how I got every other sub-faction to assist the NCR as well. At every turn I chose the option of assisting the NCR and being against every dialogue option against that goal. I told Yes Man that he should ignore every other faction, as they were assisting the NCR. However, at the end Yes Man had me gain the help of the Followers of the Apocalypse, but the only dialogue option with them was against the NCR, which to me was the first time the quest series declared by force that I would be fighting against the NCR in helping only Yes Man with control of Vegas. The assumption until this point was that Yes Man was supposed to be doing my bidding, not the other way around.

By this stage I had already saved the President for the Yes Man. However I was still able to turn in a quest for NCR, regarding the Brotherhood of Steel. When I turned in the BOS quest to the NCR, the next option was for me to Save the President (again). Obviously a bug in the quest, as this had already happened, so at this point I was unable to assist the NCR any further due to the quest not being able to progress, and forced to chose the Yes Man ending. However, as I had gathered every single faction to fight with the NCR, they all turned against me when attempting the Yes Man outcome to save the Dam. So by this stage I decided to cheat with the console and complete the broken quest for the NCR president and continue on the path I was originally planning. This to me ruined the ending, as it felt false.

So to sum this up. The missing option in this plot is to have Yes Man (that I apparently control) to assist the NCR, otherwise what is the point in helping Yes Man, as his outcome is exactly the same as what Mr. House was aiming for, which meant removing him from power was pointless, and I might as well have left him in place.

Current Outcomes:
NCR - Takes control of Vegas against NCR and house.
Legion - Takes control of Vegas against NCR and house.
House - Takes control of Vegas, against NCR and Legion.
Yes Man (player control) - Replaces house - Takes control of Vegas against NCR and Legion.

The entire game lead me to believe I was helping the NCR, and due to lack of actual descriptive dialogue options or quest notes, I was unaware that I was at the same time fighting against myself and NCR by taking the Yes Man route. The Yes Man route should have assisted the faction of my choosing, whether that be Legion Ending, NCR Ending or the Player takes control of Vegas. This would have been the logical outcome for Yes Man, as it was the 4th choice and the only one that seemed to be neutral through the course of the game.

...wait, you're saying that you never even realized you were fighting for an independant New Vegas even though Benny and Yes Man specificly stated that was their goal? You joined the revolution without even knowing it? :facepalm:

You supported NCR defenses because they're not simply another opponent, they're also New Vegas' best customers and trading partners. (Okay, admittedly House explains this, not Yes Man, but the logic still stands.)
You saved Kimball because you needed HIM to be the target of NCR scorn, not you. (Another House scheme adopted by Yes Man, though you can actually just let him die if you're independant.)

Remember, the Boomers allied with YOU, not NCR, and you can use this fact as leverage over Oliver at the end. If you wanted to help the NCR, DON'T upload the Dummies Guide to Taking Over the Mojave Wasteland. It's what causes the game to recognize you as being on the Wild Card path, though admittedly, they could have made this clearer.

Im with you on this, But I support NCR, as "out of a bad lot" they happen to be the best option, oh and im ex forces, and feel the world would be a better place, if the NCR had full control

I realised that was Benny's goal, but with the player taking control, you would think the player would have the final say in what happens. The thing is, I don't recall Yes Man stating that with me in control, I would fighting for Independence, especially as he was asking me how I wanted to take on every minor faction, I assumed the same would be done with the larger factions.

It's more about it being unclear. It would have made more sense to have the Yes Man quests as entirely up to the player to decide, as all other options are covered by the other main groups.

I agree completely. I didn't understand the yes man chain at all.

How did you find the mission ID?! I need the Mission ID for "all or nothing"..