I still believe the biggest issues are:

1. Lack of practice/training opportunities for refs. MLB umpires get 162 games/yr (roughly); NBA refs have 82. NFL refs work, at most, 17 reg season games/yr. Add to that, NFL football is widely agreed to be the toughest sport to officiate, and that lack of practice time/opportunity to get better I think makes it hard.

2. Too many rules that are 'judgement calls'. I think this is where the kinds of things Ry was mentioning really come into play, as the NFL can tell the officials 'keep the flag in your pocket' in an effort to drive up scoring. I'm not convinced on the out-and-out manipulation of games (calls becoming one-sided in a deliberate effort to keep the score close), but I would agree that the NFL is telling refs to call the game in ways that will drive up scoring overall.

But another issue with how many 'judgement calls'-type rules there are is how different one crew can call a game from another. One week, a DB can just about tackle a WR and get away with it; the next, the same exact play draws a flag because this week's crew 'calls a tighter game'. Ref A says "that's not a hold"... a week later, same exact thing done, and Ref B throws a flag for holding. There are web sites now where you can go and actually track which crew calls the game tight, and which calls it more loosely. But I think NFL players are more creatures of habit, and so it's harder than people think for them to adapt on the fly to a crew that wants to throw a flag every time you fart in the opponent's general direction...

3. Lack of consequences for bad officiating. There are some games, and some calls within games, that are so egregiously bad... at some point, the expectation should be that official X is no longer an official. But we NEVER hear about that. There is no transparency re: how officials are graded out after games (at least, not at the fan level - not sure if the teams get any info on that). And every single season, there is one crew (sometimes two) that are SOOOOOO bad, you almost yearn for replacement refs.

4. Specific to the playoffs, I think it is complete idiocy to create 'all-star' ref crews. These guys have been a crew all year... they should keep them together throughout the Super Bowl. Seems to me like there's a chemistry among an officiating crew - one knows what the other is going to be looking at, so he can in turn look elsewhere. Seems really stupid to throw that all away just when the games really start counting...