Well, the thing that seemed to bother everyone was that it was forced and seemed thrown in just for the sake of having a happy ending. Yuno isn't even the original either, just a copy.
And the hammer.
And then the fact that they get a happy ending for being terrible people, especially Yukki, since most people didn't like him and he did nothing for 10,000 years. Aaand that Deus just kinda goes "herpadurrr you ugys can be god together now".
Here are the final manga pages:
http://mangafox.me/manga/mirai_nikki/v12/c059/35.html
Now, I didn't dislike the ending, an I was happy there was a good ending, but it
was done kind of ridiculously still.
They did. It was really quiet, but right after the diary changes, turn your volume up a LOT. I didn't notice it when I saw the raw, but when I saw the subs said "Yukki", I had to check. Turning it up showed she did say it.