But most games, stories, superheroes have good guys and bad guys. We can be somewhat sympathetic and understand what Thanos did and why, but he was still the bad guy. The reason The Joker exists is because he's easily identifiable as the bad guy.
If you have a game that (at least for many people) is about heroes saving the day you need a nemesis, an enemy.
Um... your examples are individuals that don't represent their species. Not all Titans were like Thanos. Most humans are not like the Joker. These examples do not justify making an entire species "the enemy" - quite the opposite, the exampled demonstrate that extreme individuals make good enemies.
There was no need to have entire species be the enemy. That was just a simple approach that the original writers and players didn't see as a problem. It has shown to be less-than-great. It is probably time to retire, rather than justify and defend it.