Alright, this has bothered me since my first playthrough of New Vegas.
I went independent, and mostly feel I made the right choice, but what Yes Man says at the end has always made me feel uneasy about my decision.

Refresher for those that forgot:

Okay, so he says he didn't want to make a big deal of this until after "we" won.
That tells me he has been plotting something already.
Then he says he has found a way to reprogram himself using Mr. House's databanks.
This screams to me that he has his own agenda, I get that no one wants to be a slave, but he is trying to be more assertive, and I don't think it's a stretch to say he wouldn't be saying yes to everything anymore.
Which means he will essentially no longer be Yes Man as we know it, and can act upon his own plans.
He is going offline for a while, so he can make these changes to himself.
What will happen when he comes back online?
Who knows, but I feel a sense of dread based on what he said.
He is the real one controlling the securitron army, and has basically given them orders until his return.
I have no idea what this used and abused AI is really up to, but look out New Vegas!

Am I the only one that sees something is up with him?
Any other thoughts on this?

I was never comfortable with Yes Man. I always had a feeling that something was not in order with him. He seemed like a wild card to me. The ending at Hoover Dam really asserted that uncomfortable suspicions that I developed. It is rather clear that Yes Man is up to something and him becoming more "assertive" is concerning. I suppose this goes to show that no matter what ending the courier chooses, he/she is an asset to a third party rather than being truly independent. Nevertheless, this is a very open ending that Obsidian could have further extrapolated upon.

I've never actually completed New Vegas. I've come very close several times, but I usually ended up completing all of the DLC first and after that my game would CTD a lot. I've always planned to go the independent path as I like neither the NCR, Legion nor House, but is it possible to go independent and kill Yes Man as well?

The only way to kill him is to gooify or disintegrate him, otherwise he will respawn.
Apparently, it doesn't end or fail his quests, but you can't continue them really either, since he would be needed to complete that line as far as I can tell.
So, it appears the only way to complete it is if he is alive.
Oh, and I read this on the fallout wikia.

"This personality change makes him more assertive, meaning that he will take orders only from the Courier in the future."

If they don't give you this information in the game, and if the company never clarified it, then I really can't trust it.
They do a good job at the fallout wikia, but I can't see how they came to that conclusion.
At this point, I consider that to be an opinion.

TheHermit wrote:

I've never actually completed New Vegas. I've come very close several times, but I usually ended up completing all of the DLC first and after that my game would CTD a lot. I've always planned to go the independent path as I like neither the NCR, Legion nor House, but is it possible to go independent and kill Yes Man as well?

I'm afraid not.

If you want an independent Vegas, you have to choose between House, a technological genius who saved the city and has managed to restore civilization into the city, and Yes Man, a suspiciously friendly robot who, as said, will basically be holding power over the Securitron army and has plans of his own.

Seems to me that the House ending is the best. You get an independent Vegas, and as much as I like my own character, I'd say that he's more qualified to govern the city than some random dude who wandered in from the desert after getting shot in the head.

All in all, he's more benevolent and qualified than the other factions, and the only one that has actually built progress and well-being in New Vegas. I never understood why some people don't like him.