1) Knowledge. In times when God reveals himself more clearly through his actions, people are held responsible for that knowledge. God had been displaying his wonders through his acts of kindness toward Israel, therefore the peoples who lived closest to Israel were held responsible with more severe acts of judgement. Egypt was one example, with an escalating series of miracles making clear the extent of the Egyptian people's rebellion against God. In 1 Samuel 15, the Kenites are warned to not assist the Amalekites or be included in his judgment against the Amalekites. They are also commended for assisting the Israelites in the past, whereas the Amalekites had always been hostile.
2) Patience. The Amalekites oppressed Israel for centuries, yet God held back, giving them a chance to change. As a more extreme example of God's patience, consider the people who lived during the time of Noah and were wiped out by the flood. They were warned well in advance, but refused to change. Methusaleh's name means "When he dies, it will come." His name is a prophecy of the coming wrath. If God were long on justice and short on mercy, he would have made Methusaleh live a short life. If long on mercy, he would bless Methusaleh with a long life. Which did God arrange? Methusaleh lived 969 years, longer than any other human in all of history. God chose mercy - with a limit.
3) Unselfishness. When executing God's decrees, Israel was not to profit. They were doing this for God, not for themselves. That is why the animals had to be slaughtered. If they took the animals, they would face a moral hazard - profiting personally from the eradication of other peoples. There was a battle fought by Joshua that they lost because an Israelite took some treasures as plunder when they were commanded not to take plunder.
4) Impartiality. When the people doubted God's goodness in the time of Moses in the story of the twelve spies, he permitted the Amalekites to defeat them in battle. In that case, the Amalekites were instruments of God's judgment against Israel. This shows that since God favored the Amalekites when they obeyed him, he had set an example for them to follow, that if they obeyed Israel's God, they could expect favor and mercy; He is a God for all people, not just one nation. God did the same for Egypt, sparing them from famine through Joseph, but they later repayed grace with slavery and infanticide. God also prospered Babylon and other empires, only to overturn them when they refused to turn from evil.