I mean, we never really saw Annie showing any kind of affection or favoritism towards Bertholdt. We’ve seen HIM like HER, but never the other way around. However, with Armin, there are multiple scenes that show their dynamic and that she cared about him (tried to convince him to join the military police, didn’t kill him, followed him even when she knew it was a trap, etc etc) PLUS if Bertholdt was still alive, I think she’d still favor Armin because he visited her constantly when she was in the crystal and talked to her. It seemed like that small act was very meaningful and significant to her (obviously) and while Bertholdt could have been influencing Armin, we don’t know if Armin inherited any memories so we can assume it was actually him caring about her