For this I’m going to break the “like” distinction into character development and character appearance.
I like manga!Helios’ design more, mostly because I never liked the look of the horn and the manga is more consistent on when it shows up (i.e. when Helios is under Nehellenia’s curse) and when it doesn’t (i.e. before and after the Dead Moon threat). However, I like the character development of anime!Helios more so than manga!Helios. I think the anime had and took the time to fleshed out his personality, while the manga focused more on developing the main cast and kind of neglected the supporting characters.
With Chibi Usa, I prefer her manga incarnation in terms of both personality and character design. I feel like her physical growth (i.e. growing taller) is more pronounced in the manga, and in terms of character growth I feel like her growth to becoming a leader in her own right is more complete at the end of the manga than at the end of the anime. Also, we get to see her in her own distinct princess gown and her eternal form, something that we never saw in the anime.