The Saiyans in Dragonball had the ability to move so fast they left an image of themselves behind.... Vegeta SOMEWHAT hinted in Namek Saga that Saiyan eyes are able to track fast movements but not predict them. Could be a similar concept (I'd link it but I'm not allowed to by rules. Just check the fight with Goku and the Ginyu Force).
Now I know Dragonball is unrelated, but here are a couple of thoughts.
1. Naruto can sense evil intent. Meaning that he can even sense Kakashi someone GOOD in this form, because almost every human has a little bit of evil intent in the manga. It's what gets them able to kill others.
2. Like I said above, it's likely that his new body lets him adjust to that speed.
3. He may be able to see the movements, but it was stated that when Sasuke or Kakashi ran at that speed and experienced tunnel vision, he couldn't see the COUNTER, but maybe the attack. It's likely that Naruto's reflexes are now fast enough to counter without being able to predict movements or see properly.
4. You're reading too much into this and Kishimoto simply made a minor plothole that has no bearing on the story.
5. We've never actually seen anyone counter or react to speed like Minato's and Naruto's.
Sasuke was BARELY fast enough to counter Raikage due to his Sharingan and him being one of the faster characters. Anytime Minato faced anyone, they'd have a stupid look on their face as he got behind them and set up some half ass defense. People like Itachi, who can use Susano'o to cover his back are more lucky than those with no defense from behind them.
Also, Naruto is not faster than FTG. There is nothing faster than an instant. Short distance, as in a battlefield, he's likely the same speed as Minato. But if Minato had a seal in Kumogakure and he was in Konoha along with Naruto, and they both had to race to Kumogakure, Minato would get there first.
