These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Green Lantern. Under Geoff Johns, Hal Jordan and the Green Lantern Corps have become the center of the DCU. Yes, bigger than Superman, Batman, and Wonder Woman is the Green Lantern. At least for a while.
Superboy Prime, to the point where he is considered unreadable when someone else writes him. Case and point: Countdown to Final Crisis
The Flash had most of his villains redone, starting with a strongly anti-hero Captain Cold, spinning through most of the Rogues' Gallery. Everyone was adjusted and made deeper, with their personal storylines continuing. Perhaps the most drastic change was the death of the first Captain Boomerang and the rise of his son to take his place.
And Parallax. In fact is it safe to admit that he has pretty much made Green Lantern the most consistently good comic of the last 5 years?
In one issue, Johns took the Tattooed Man from a joke to an anti-hero powerful enough to earn his own mini-series. (Admittedly, it took giving someone else the name and powers to do it, but the new Tattooed Man is still awesome.)
With the revival of Barry Allen being a bad example. His death was a big moment, and most readers got over it. They had 20 years to do so, and Wally had become the Flash for two generations of readers. He really didn't need to be brought back, unlike Hal Jordan, and his revival also led to Flashpoint, which led to the erasing of Wally West from existence...
Though whether or not erasing Wally West from existence was something he actually wanted or forced on him by way of Dan DiDio's Executive Meddling we will probably never know...
His treatment of Swamp Thing prior to New 52 (which pretty much scrapped everything about the character from the start of Alan Moore's run onwards) wasn't exactly well-received either.
He's got a pretty well-documented axe to grind with the Kyle Rayner incarnation of Green Lantern, and tends to go out of his way to undermine the character (up to and including having a villain in a Booster Gold story set in an alternate future bring up how much harder it was to kill Hal than Kyle apropos of nothing). To a lesser extent, Johns tends to treat any character/concept from the 1990s as disposable, though of course that's not always a bad thing.