Shouldn't they also know when to use the correct attacks automatically as well? Some times dodging isn't what they should be doing but countering the attack, blocking it with moves like Protect, building up for another attack that takes 2 turns i.e. Solarbeam. So it is up to the trainers instincts for what the pokemon does. Of course if you have something coming at you there is probably a natural reaction to steer away from it, but the trainer may have other plans and dodging doesn't fit into that said strategy. It's not like they loss their instincts to dodge it's just following the trainers battle plan.
In Super Smash Bros. Brawl, the Colonel from Metal Gear Solid tells Snake that the Pokemon wouldn't know what to do if their Trainer isn't their directing them.
So obviously the Pokemon don't have instincts or whatever. They rely on their trainers.
Exactly what I was going to say. We have seen trainers in the past who have their Pokemon stand their ground which in most cases is because they have a way to counter the move or will use it to their advantage. That being said, we have also witnessed Pokemon dodging moves without the need for a command. It really reflects the trust between trainer and Pokemon as the later will follow the trainer's plan if they trust in them and the same vice-versa. And it makes the battles sound more "exciting" (even though not really most of the time).