When asking a question about the difference between the manga and anime, I would have never thought to use the variations tag. Can we create a synonym of this tag as anime-manga-difference, or at least differences?
I'm not a fan of anime-manga-difference. Of the 9 questions tagged as this, 4 of them aren't about comparing anime and manga. It would quickly get out of hand if we had tags for every pair such as light-novel-anime-difference,anime-movie-difference, visual-novel-live-action-difference (okay maybe the last one is unlikely, but you get the picture). Furthermore, it's not clear what should be done if there are 2 different versions of the anime. If I wanted to ask what the differences are between Eat-Man '97 and Eat-Man '98, would I use the tag anime-anime-differences? That's just silly.
I don't have a strong feeling one way for differences vs. variations, but it's not clear to me that the former is more intuitive than the latter. I'd be very surprised if new users use the correct tag regardless of which we choose. From a practical standpoint, I'm just slightly in favor of keeping the status-quo, simply because people are already using it and may not notice the switch.