Yeah, having your undead minions having a weakness for plot resolution is a pretty critical design flaw, but apparently Kabuto wasn't aware of it until now.
He can't with that lightning sword in him as lightning style disarms his explosions.
You are mistaken, they stopped talking as soon as he put the daggers in them.
But yes, I believe this is essentially the main difference. Killing off their emotions gives the user complete control, but then you have to focus on them much more.
In order to have an entire army of zombies, he's leaving them their personalities so they can control themselves to a degree, but they still have to obey his commands.
It's an interesting tradeoff. Complete control over a couple zombies, or vague control over an army of zombies who are weak against closure.