Except that he attacked and genocided allied nations as well.

Not yet, unless they've released the second half of the final season.

And he also just killed billions of innocent people who had nothing to do with their governments policies and were heavily propagandised for a century.

Sure, but that's just war for you. The last few episodes had what amounts to a civil war breaking out on Paradise, with a number of the main characters turning on or subverting one another.

Also the Eldians had a brutal empire which likely practiced apartheid and suppressed non Eldians.

Ages ago. Modern Subjects of Ymir are locked in ghettos unless they agree to join the Marleyian war effort. In some of the flashback scenes they're even dressed like ghettoized Jews. Nevermind how many Marleyians are explicitly German coded with the blonde hair and blue eyes.

Might as well say "Jews are the real fascists because of how awful the Pharisees were"

I kind of did like the fuck around and find out part of the story when the rumbling started initially on Marleys face but it soon became a far bigger thing which was just horrendous.

The original set up of the story is a conspiracy by the king to effectively euthenize the existing population. As the seasons unravel the mystery, you begin to see the deeper motivations of the various characters. And this all culminates in the revelation that the Subjects of Ymir are the cursed self-cannibalized offspring of a ruthlessly exploited slave girl.

The story is endlessly harping on the horrors of war, the hubris of ambitious men, and the horrible errors we make by acting rashly on incomplete information.

Eren's Rumbling is the culmination in a nightmarish cycle of wars, enslavements, and bloody uprisings that become genocidal wars themselves. Each faction has some history or social narrative that justifies its subjugation or extermination of the other. Each faction has some enthusiastic hero whose initial climb to power is viewed as liberating, but who ultimately becomes more erratic and dangerous as they accumulate authority.