especially on those that have over a hundred comments lol. people are use to how it is now but like you said other sites are flipping them so i think they will get use to it pretty quickly since they will be seeing it that way elsewhere in my opinion having the newer comments at the top is easier to check them i think you should give it a go. if it doesn't work out right or no one likes it you can always switch it back
Well, being completely flat, it probably wouldn't work here as coherent discussion would be nearly impossible.
I'm not a big fan of timelines either, though. Once you have thousands of people commenting on one post, the majority of comments end up being very low-substance (See: YouTube's comments).
Perhaps, like the front page, you can prioritize comments by people you follow over everybody else (and have an expandable quote system like Twitter has)
That always throws me off cause so many websites do it differently from another. I'd say stick with what you have now. By now most people are familiar with the comment layout, changing it would cause more confusion than anything in my opinion.