1. The ball: maybe it hasn't affected play, but maybe it has (and FIFA has admitted as much now), but who in their right mind thinks it's a good idea to introduce a new ball with distinctly different performance characteristics right before the finals of a tournament?
2. Vuvuzelas: as I said before elsewhere, if it's true that they're "absolutely essential for an authentic South African footballing experience," then I guess it must mean that footballing in South Africa blows (literally, even, I guess). At first I was willing to give them a chance, but no, there's nothing really good about them, they're just annoying. They drown out everything else, songs or what have you, and make it impossible to communicate on the pitch. If I was a foreign fan who traveled all the way to South Africa just to get deafened, I'd be mighty pissed, and as someone who'd like to see a cup in person someday, I'm glad I didn't pick this one. (Yes, we've all seen them carried by international fans, but I imagine it's as much giving in to the arms race of noise than anything).
FIFA, of course, doesn't consider them to be a problem.
3. The region selection: why does Africa get more automatic bids to the finals than South America? How does this remotely make sense? In fifteen group matches, the South American teams lost one game. One. (And they haven't lost any since -- tonight will be the first, but only because two South American teams are facing each other. And, most likely, Chile will remain the only South American team with even a single loss.) Of the five South American teams, four won their group. Every one of the five advanced. It's conceivable that all four teams in the semifinals will be from South America -- it's fairly likely that three will be.
Meanwhile, in eighteen group matches Africa has managed all of three wins -- to ten losses.
Of the two South American teams ranked in the top 32 (by ESPN before the tournament) that missed the cup (namely, Ecuador and Columbia), both were rated higher than all but two of the African teams that did make the cup (including one team that lost all three of their games -- Cameroon). Of course, neither team was the single African team that actually did manage to advance (Ghana instead of Ivory Coast or Cameroon) -- and judging by actual performance in the tournament, you get the idea that the African teams are if anything actually over-rated.
Of course, FIFA is on record as having no plans to change the continental lineup. Which I suppose is good for the other teams that did qualify, since they'll continue to have African patsies to beat.
4. Finally -- and this is the big one -- the officiating has been a travesty. Any number of goals have been erroneously called back due to bad calls, most unbelievably, England's clear goal against Germany, which completely changed the complexion of the game. Germany might have won anyway (probably would have, they were the better team on paper), but the result remains tainted. Same for Argentina-Mexico, on a blown offsides non-call. The USA came out best here -- despite having two goals called back on calls ranging from close but probably wrong to completely inexplicable, they won their group anyway, so were largely unaffected. And that's just the goals.
But so far FIFA has remained opposed to anything that would improve the officiating at the games, from bringing in overmatched refs in the cause of "diversity" to defending the gaffes as necessary for the "human" element of the game. It's idiotic; the players are already plenty human enough, but we're in the 21st century now. There's very little excuse not to get the officiating right when every viewer can immediately seen that the ref blew it. Not in baseball, not in soccer.
FIFA's response? Ban replays in the stadiums so the teams and fans in attendance won't find out they were robbed until afterwards. Yeah. That'll fix it. In the meantime, when the refs have no accountability at all for blown calls, you can't help but wonder if some of the games were actually fixed in the process -- it's really hard to distinguish malice from incompetence, and with the amount of money involved, it's hard to give the benefit of a doubt. And FIFA hasn't done much of anything to earn it.
...The other ugly thing about this cup (and about the game for a while) are the dives. There's really not much excuse for it anymore -- they're fairly obvious on replay. And they wouldn't even need to sanction players during the game; assigning a red or yellow card after the game for sufficiently egregious cases would probably go a long way towards getting them under control.
Of course, we'll see if FIFA manages to fix anything, even the easy obvious stuff. I remain skeptical.