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That's the problem though. They had two different wars. What happened in these wars? Why were they fought? Was anyone else hurt? How long ago were they? Lt. Surge seems like he was happy to fight in the war, so it's not like it was anything heart wrenching. Keldeo's parents died... but once...
The problem with the games isn't the villains themselves. It's the fact that there is absolutely no reason for them to believe any of the things they do because the Pokemon world is a utopian society?
Want to wipe out humanity? Why? Because there was one war a thousand years ago that you didn't...