Everyone will suggest Anemone just because its purpose is to replace Themely (And because it being mainstream). But personally I don't feel that it fully replaces it just yet. It's lacking in some features that Themely can do right now. That being anomone cannot preview theme music, which is the best part of themes. If you don't know what music is involved, you wont know if you like the theme. Unless you prioritize the background more than anything. The next thing Themely can do is show icons for every theme, even themes that never had an icon. it takes preview.png and makes a temporary icon out of it which is helpful for looking through your themes. Anemone will just show those themes with blank icons. This is problematic because sometimes you'll end up having two themes called Mega Man, but both are different themes entirely. The icon helps to distinguish them so I know which mega man theme its referring to.
However Anemone has an advantage, being able to mix match music from different themes. This is only good for users that use one theme rather than shuffle themes. Personally I always shuffle 10 themes and enjoy their music whenever they show up on my home menu. The next advantage of Anemone is that it can manage splash screens for luma3DS. Makes it much easier to swap between different splash screens instead of doing it manually.
In the end you could use either one as they both work the same for installing themes. I keep both installed on my 3DS but mainly stick to Themely for now (Actually, I use the fork by Favna. Its called "3DS Theme Manager"). I have no doubts towards Anemone though, the developer is having an extremely busy life and can't work on it. That's why it hasn't received updates in over a decade. All the things I mentioned are planned features so they're noted. It's either gonna take his free time, or someone will fork it and continue it. But for now, the lack of being able to preview music is a deal breaker for me and I cannot suggest it to newcomers whom I help to hack their 3DS.
At the beginning of the post I mentioned "mainstream" because some people like to blindly follow whatevers new and popular. Like how people suddenly consider the 3DS and Wiiu to be complete shit just because the switch is out, hoping those systems just die already because they have a switch now (Not everyone has a switch you know). So basically I'm focusing on Themely's features, not its drama involved with it. And that's everyone's motive to even suggest Anemone at this point. I don't care one bit about whatever happened there.
