I'm still of the opinion that Wily is Chaotic Neutral at the very worst. He's dangerous because his [parasitic bomb] works and he doesn't give any fucks about collateral damage. When you combine that with the idea that he's making or manipulating high performance combat robots for his own gain makes things all the more insane to deal with. This doesn't mean that he doesn't have merits as seen by MM10 with his silent donation of the Roboenza cure after his defeat and hospitalization. There's also the idea that throughout his character's history, he's explicitly referred to Light as his rival which suggests that there's a respect there even if he would probably prefer to win more often. If he has decency enough for that, it becomes harder for me to see the character as evil beyond "token villain" status.
Don't throw anything Zero/Virus at me either, I'm still of the opinion that the Virus was both Wily's soft spoken will for as well as a power source developed only for Zero that got a bit wonky once Sigma got exposed to it and changed its purpose unintentionally.
Wily just seems to be a highly intelligent opportunist with a bad luck/bumbling streak and he's charming as a villain for that much.