I think one of them is that Justice League reverts to a quite simplistic moral view, almost Super Friends-esque; whereas Man of Steel and Bats V Supes tried to present these characters in more realistic fashion where everyone has shades of grey, and even acts of heroism have consequences. Justice League totally avoided that.
Super Friends-esque?
I mean, a decent portion of JUSTICE LEAGUE deals with the consequences of Superman's heroism...his death. The film talks about the impact the crusade has had on Batman, Aquaman rejects outright heroism, Wonder Woman details the nature of leadership and heroism; sending people into battle, the personal risk and her conflicts with this...the film doesn't delve into "gray area" themes as much as BVS or detail the public's reaction to things, but it certainly doesn't avoid any of the more serious aspects of heroism, either.
The two previous films went to great lengths to establish that, despite his state funeral at the end of BvS, Superman would be loved by some people and feared by others, that he'd be a controversial figure.
That is really not the message intended by the end of BVS. The point of the state funeral and the mourners is that he is largely accepted in death because of his sacrifice. He is, more than ever, one of them and accepted as such.
He was controversial, but that was before he essentially "proved himself" to humanity. There's no reason to believe there would be the same level of controversy immediately upon his return, and even if there was, the film doesn't deal with this anyway.
JS gives us a very simple, smiley, beacon of hope Superman, which doesn't make a lot of sense given all that has happened. It's the Superman audiences wanted, but it's not the Superman from the previous films.
I guess you missed the part where he's confused, angry, conflicted Superman for a bit there.
He's actually not that complex in BVS...he's still a pretty straightforward hero with straightforward desires to save people. The issues surrounding him. in terms of his relationship with the world, are a bit more complex...but those issues are essentially resolved at the end of BVS.
The fact that Clark cracks a few jokes in JUSTICE LEAGUE and not so much in MOS and BVS does not mean the character was never capable of doing those things...that simply wasn't the focus of the film. Even mostly serious people can make jokes if they're in the right mood.