I think it's a matter of opinion, I like Skye as I like her aesthetic and her colour palette and just all wolves in general but if she doesn't appeal to you that much anymore i'd go ahead and get rid of her. I know what you mean though, i've had villagers I thought i'd keep to the very end and then I just started to find them.. very unappealing. So I got rid of them. I'd go for Fauna, I'm not a huge fan of the deers but I can say that she is quite cute. Especially nice to use in woodland towns/villages. I don't know if it's just me but I get the feeling that Molly has become somewhat overrated I guess i've seen her a lot in dream towns and other peoples villages, and I've never seen the appeal of her.
I voted before I read the OP and voted for Skye! I think if you don't like Skye you should choose who will best go with your town. Both Molly and Fauna have a lot of similarities. I think I like Molly a little more because I like how the ducks look walking around in the rain.
I think Molly is absolutely ADORABLE and might be one of the cutest villagers in general. With that said, Fauna just feels like so much more. I think she's a little less adorably cute than Molly, but shes much more aesthetically pleasing to look at. Not to mention her personality is just so cute and lovable