A couple with Jason.
First, no longer being the Dick clone, as mentioned above. The second, was developing his character with New52 (though leaving UTRH canon, almost everything else pre-Flashpoint was erased).
Damian getting people in his "own group", so to speak, to interact with. Maya, Jon, the current cast of Teen Titans... Yeah.
Supes and Lois becoming parents. As divisive as this seems to be, Jon was a great addition to the family and Clark learning how to be a father along the way (early Trinity Rebirth did a great part where it showed Pa Kent learning how to be a parent to Clark while developing powers).
Axing Super/Wonder. Never liked it, and made me feel very uncomfortable. And this is probably not going to win many points amongst certain Super fans.
Getting rid of the sex pirate Amazons. It just ran so counter to what the Amazons had long stood for, I was happy to see it go.
Bruce and Diana guarding/being there for Jon's birth at the end of Superman Reborn. Prior, Jon was born during Convergence, making the Kents rather odd. With it though, it showed the tight friendship between the Trinity.