I personally prefer the V2 home, mostly due to the latests updates being in a list format. The 2-columns forces me to move my eye in an awkward zigzag movement, which makes it very hard to focus and see the updates. In the list format, I can just lock my eye in a part of the screen and scroll, and then I can very quickly see what's new. As an example, compare how quickly you can find the volume/chapter's number in each layout.
And yes, I know about http://beta.mangadex.org/updates page, but that one doesn't have the other stuff like top chapters/manga, and it's a also quite hidden (takes extra clicks to get in ther if I'm in a page other than the home).
I'm also not a fan of having the comments in the home page. They don't really bother me since they are quite low in the page and I know I will very rarely read them, but even if they are not comments from chapters, spoilers definitely will happen. People just expressing their feelings about a recent development in the story could accidentally give a hint to someone who's still browsing the main page before going to read the latests chapter.
Lastly a nitpick: I think the topbar blends with the page too easily. It would be better to either bring back the dropshadow, add a border or increase the color contrast.
Sorry if I didn't have many good things to point, but I at least tried to make it constructive.