Thinking about it, some of the other issues in addition to what I mentioned are this.
Batman is an asshole.
Shortly after Zero Hour, I read a team-up between the new Starman, Swamp Thing and Batman (something about restoring Solomon Grundy). Throughout the first issue of this team-up, Batman was an unrelenting asshole to everybody. I asked my friend who was into Batman what was wrong with him and he just said that this was what he was like in all guest appearances now. Unfortunately, this idea spread until it started hitting his own comic as well. Everybody tries to talk about what a great humanitarian Bruce Wayne is and how vital a part of the JLA he is. However, except for brief moments, he's portrayed as a whiny asshole who is a massive control freak. Every time he doesn't get his way in the JLA, he quits or just does what he wants anyway. Batman used to work with the police but now he just does whatever he feels like and everybody just goes along with it. At some point, having a Batman who is a completely anti-social asshole should come back on him hard.
Perhaps this is due to the readership. Maybe the Bat-Fans are people who are completely impotent in their real lives and they enjoy reading about a Batman who can do anything and treat everyone else badly. Perhaps this is due to lazy writing. Whatever the reason, this is something that has to stop. Batman has to learn to play nice with the people who are his allies.
Power Creep
I realize that I mentioned how Batman could use his wealth more creatively but I want to revisit how his infinite wealth becomes two character flaws.
Pre-Crisis Batman was still just an "old money" rich boy. He had a finite level of means. Post-Crisis Batman now has an infinite bankroll which he can use to create Batman Inc/Satellites that spew forth self-replicating robots/The Watchtower/etc
Yet, Gotham is still a slum.
When Batman is established as having enough money to outright buy Gotham and improve the city immensely but he chooses to just punch people in the face, this becomes a character issue. The issue becomes more dramatic when you realize that all of the people he is beating up are either the poor or people who have stereotypical representations of mental illness. I imagine that this is one of the reasons that the goons in Batman are all white males. Having an issue where a rich white boy in a bat-suit beats information out of a poor black man might set off a massive ****storm.
This is simply lazy writing and needs to be cut out. Personally, I would like to see Batman go through the same thing that Tony Stark did ages ago where Stark lost everything and was living in a cardboard box. I'd like to see a Batman who wasn't just able to reach in his utility belt and throw diamonds at people but had to make do with limited means. I'd like to see a Bruce Wayne that had to actually address the money side of issues and had to spend time actually running Wayne Enterprises. Somebody who actually has to interact with people without the cape and cowl AND without being able to punch his way out of a problem.
Lateral Thinking
As I said earlier, Bruce Wayne needs to start finding more creative ways to help the people of Gotham than just face-punching. Believe it or don't, Pre-Crisis Batman had whole issues devoted to him helping through philanthropy. Sometimes, it was a convoluted way to flush out a criminal organization (The Kangaroo Race story comes to mind here) but, sometimes, it was also a way to say "Hey, funding a free clinic so people don't have to turn to crime in order to afford medical aid helps cut down crime."
When is the last time Batman actually thought this laterally? When is the last time we actually had Batman look at the conditions that make a white male say "Hey, working for the Joker is the best career path available to me." and try to address them in a non-face-punchy way?
If we MUST keep the infinite wealth angle, I'd like to see a Batman who occasionally uses that wealth for something other than diamond-encrusted Batarangs. It doesn't have to be every issue. Most issues of Pre-Crisis Batman didn't focus on the philanthropy either. Just every so often, use it as a way that Bruce Wayne can help Gotham in a way that Batman can't.