First off, it's IMPOSSIBLE for you to have YEARS of research, given the fact that Undertale has only been out for a little over a year. Secondly, there is a reason that Flowey is talking to Chara. To explain this, I have to explain a bit about the naming. Since Chara is obviously the name of the first fallen child, why give you the ability to choose their name? It's because Toby Fox WANTS you to name them after yourself. This is because you choose what becomes of this child. Your choices affect this character. And with this in mind, going back to Flowey talking to Chara, he doesn't know that you're the one who's been in control of Chara. He know that Chara's been doing this, and so he talks to them. But if you name Chara after yourself, he's also talking to you without knowing it.

Now, onto Chara wanting to kill the humans. There was reason. Chara wanted to kill the humans, to get their souls to free the monsters. They made a plan with Asriel to go to the surface together and get the souls they needed. For this plan, Chara KILLED THEMSELVES by buttercup poisoning. And so you know, buttercup poisoning is a terrible way to die. Symptoms include blistering skin, intense burning of the mouth and digestive track, bloody diarrhea, and more. Yet Chara put up with this, just to set the monsters free. Then they went to the surface, and the humans attacked. Chara tried to get Asriel attack, not just to get the remaining 6 souls needed, but also to save their lives. Also, you say that wanting to kill ALWAYS makes someone evil? So Undyne is evil? She wanted to kill you. Is she evil? And Asriel. Asriel wanted to kill you. Are you going to call Asriel evil?

Also, in the ending where Chara asks for your soul, yes, they do take Frisk’s, but that’s because they can’t take yours. You and Chara are separated by the screen. They can’t take your soul, so they do what they can, and take Frisk’s soul. This means that you can never have a true happy ending in the game again.

For the whole thing with other games, it doesn’t apply there. The game was made with different minds, for different reasons. The logic of Undertale, isn’t the same logic of Mario. Mario was made to simply be a fun game. Undertale, was made to be something more. And yes, of course you didn’t do these things with your own hand. But you where the puppeteer. And if the puppeteer controls the puppet and makes the puppet kill a man, who’s guilty, the puppet, who had no control over its actions, or the puppeteer who used the puppet?

And with stats, you may think, “Oh, since all the stats go to Chara and not Frisk, surely Chara’s evil and Frisk is nice”, but that’s not true. Just because Chara receives the stats, doesn’t mean they want to. Let’s say I come up to you and forcibly cut your hair, and there’s nothing you can do to stop me from cutting your hair. Does this mean that you wanted to have short hair? No. You were forced. The same thing happens with Chara. They have the stats forced onto them and can’t do anything about it. So after realizing they can’t stop what’s happening, they help you. Just like you helped them get to that point.