Sure, in the end he did (literally) overthrow Palpatine. And in Episode III he mentions it to Padmé on the Mustafarian landing platform. The question in my mind is: was this a continuous desire from that moment right up until he chucked the Emperor down the shaft, or not?

Remember that the line in Episode III came before he got baked and put in the suit. Psychologically he was a different man.

After his transformation he would have been stewing in some pretty serious bitterness and self-pity, and to some degree felt he owed Palpatine for saving him from the lava beach. This may have helped negate his initial desire to "off" the Emperor.

Much like a psychologically abusive spouse, Palpatine would have had ways to manipulate Vader into staying with him. Look at all the plotting that went into corrupting Anakin to begin with--once there it would be a comparatively simple matter to keep him on the leash, periodically setting him loose on some Rebels or leftover Jedi or incompetent admirals, to take out his aggression on.

But eventually he realized being Palpatine's b!tch wasn't all it was cracked up to be, and that's when he resurrected his old notion of revolution. Yet he knew firsthand how powerful Palpatine was, so even after he hatched the idea he would have been very careful to get all his ducks in a row before moving against him. Enter Luke Skywalker, and suddenly the timetable accelerates.

I'm sure Palpatine milked "I rescued your crispy torso and put you in this position of incredible power, so you owe me" as much as he could. But by the time of Episode VI--after Vader had been living under Palpatine's heel for 23 years and now he knew he had a son--that just didn't cut it anymore.