but the konoha villagers are still alive. Even though pain attacked konoha, he brought them back to life and there wasn't any direct attack from madara during those sixteen years. When he had the organization to destroy nations, itachi stood in his way.
Do you think minato is some kind of Psychic or something? all minato knew was that one day that mask man would return to attack the konoha village again. Minato had no idea whatsoever that madara was going to make the akatsuki, kill uchiha clan etc. He left the task of killing this mask man to his son.
Minato as a hokage had to protect the villagers from the nine tail demon fox.
The fact that minato seal the nine tail demon fox into his son suggest that madara/tobi/mask man wasn't around to stop minato.
for madara/tobi/mask man, it would have been better if itachi didn't kill the entire uchiha clan because he wants war but since itachi found out about him, he had no choice but to accept his offer. Madara/tobi/mask man is obsessed with the idea of having war.
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If he can't get the nations to war against each other again, he will make one himself.
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Just like I don't know whether madara/tobi/masked man got defeated with that rasengan although I doubt it. You don't know whether "that" jutsu is not FGT jutsu.