I've never actually fully made it through the New Vegas main story, mainly because I don't want to face the definitive ending. Mainly what's going on is that I want to side with Yes Man and go the independent route, but I've read a lot that New Vegas ends up much horribly off than it would have when you side with Yes Man. How can I go the independent route with a positive outcome, and still be idolized by the NCR? I really like the NCR.

Re-cap: Can I side with Yes Man with a positive outcome, and still be accepted by the NCR. If it is possible, how do I do it?

No. by choosing Independent, you bascily saying " [censored] you NCR and Legion, I own t3h Vegas"

If you upgrade the securitrons you get a better ending that sounds less terrible. Things still go awry initially, though, according to the ending. Anarchy breaks out, but the securitrons maintain order far more quickly if upgraded. Really, though, none of the faction endings suggest anything good or bad unless you're Bad Karma. Good Karma Legion Couriers, for instance, just have Caesar waltz in and take over Vegas and mint a coin in your honor. That ending in and of itself says nothing about how good/bad things go.

I thought my endings were all pretty positive.. I stuck with Yes Man.. but also kept NCR on my good side. I had good Karma with every faction accept the Legion. I had wild child Karma (or whatever that wishy washy Karma is called) with the powder gangers by the end.. so they wouldn't attack me either.
I basically went through every quest being as helpful as possible and doing the svck up thing up until the point that a faction quest would interfere with another faction. Then I'd simply make the decision as to who I thought was the more evil of those competing factions and would side with the one I thought was good. Most factions actually don't interfere with one another and you can do their quests up until the end.