I think people didn't buy Karli as the villain because they were clearly building up John Walker as the twist antagonist until they got scared and walked it all back in the final episode with an unearned redemption.
Cap vs. anti-cap is way more compelling than an idealist young left wing woman who randomly decides to start killing people, just because.
I think that was never the intent, sadly, because comic US Agent is a hero and Flagsmasher is a villain. Instead, US Agent turning back from "evil" was always meant to be the twist.
If they wanted a full on evil Cap, they would have used the Grand Director.
Besides, Karli was threatening Sam's family and plotting to kill US Agent pretty early. I feel like they should have indicated it was Super Soldier serum, though. She was never meant to be a good guy--just following a good cause.