Things subject to replay are on a whitelist. If it's not on the list, you can't review it. Most penalties are not on the list because ... well there isn't really a good reason other than a general dislike of stopping the game to review everything.

But given the roughly 30 seconds between every play, there should be enough time for some sort of automatic replay review of just about every play. At least an official in the booth (or in NYC) who can use those 30 seconds to decide if the play is close enough that he should buzz the game officials and tell them to take a timeout.

But I think penalties would be a big problem. What do you do about a penalty that was never called on the field? If you believe the adage about holding occuring on every play, that's a lot of random stoppages. I think penalties would have to be reviewable only on those where a flag is thrown. They could be overturned or upheld, but not initiated from the booth. Then you'd have to train the refs to err of the side of making ticky-tack calls, and you'd see way more flags on the field just in the first place. Consider the missed PI call in the LAR-NOR game. If you believe the story, the ref didn't throw the flag because he thought the pass had been tipped at the line and hence there couldn't be PI. Even if a booth review situation that doesn't become a penalty.