They can develop and grow from being outdated tropes while still being villains. The best villains are the ones who have a lot to say about the heroes they fight. They don't have to be pure evil either. Most bad, even evil people don't see themselves as villains right? They can do horrible, monstrous things, for perfectly valid, understandable reasons. And by making them all into heroes you take that away and the important role they play. Ivy, for instance, is a great villain because her motivations are so complex and interesting. Someone who commits acts of terrorism and kills people, who'd like to see most of humanity wiped off the earth because she's connected to a collective consciousness that's intelligent and alive but that most of the human species is entirely unaware of, that she can feel when its in pain. And she feels it all time due to humanity's constant destruction of the environment.
So she's devoted herself to protecting the green by any means necessary because to her, killing plants is no different that murdering human beings, and plants have treated her far better than human beings ever did. So why shouldn't she do what it takes to protect the environment, especially when, in her eyes, the world would be better off without humanity anyways due to all the destruction and violence we cause. Compared to a world that is nothing but green and plant life like that existed before animals and humanity existed.
That motivation is great, because in a lot of ways, she totally in the right especially in the context of the world she lives in. She just takes things to an major extreme due to the trauma she's suffered from people like Jason Woodrew who tortured and manipulated her, driving her kind of mad and making her hate most of mankind. Which is what makes her a compelling villain. As well as a great Batman villain because she is someone who suffered tragedy and trauma, and choose to deal with it in a negative way by hurting others instead of in a positive way like Batman did. Doing away with all this strips away a lot of what makes her fascinating, and also continues the trend of little to no diversity among villains in comics. Which I don't find to be healthy at all.