Six Feet Under as a series didn't live up to the hype for me. I disliked most of the characters. The finale though was remarkably good. The entire episode wrapped things up very nicely and the final 10 minutes was amazing.
BB was a far, far better series but if you're only looking at the finale my vote is Six Feet Under.
I think Nate was hard to like at times, pretty much because he was kind of an #####, but he had moments where his inner kindness did come out, like when he came back to work with David after the latter was having trouble adjusting following the carjacking. And the scene where they bury Nate is just soul-crushing.
And I think David was very likable. It was weird at first to see Dexter kissing guys

(I watched SFU after Dexter), but Michael C. Hall did a fantastic job playing him, and I think Hall's natural charisma helped make David that much more likable.
All in all, while all of the main characters were deeply flawed, as we all are, I found it easy to root for most of them.