So I finally got around to playing Skies of Arcadia and making some progress.
I first went with Dreamcast emulation but it seems to still have some minor glitches in Flycast, the dof or whatever effect in the intro is broken and there were some transprency issues in a single area. Very minor but eventually I also was unable to save after rescuing Fina, it said that the save was corrupt so I then tried to save on the second slot and the game hanged so I lost some progress there. If I knew this is possible I guess I could be using save states instead though I generally don't utilize such things. After rsetting the save that was supposedly corrupt could be loaded though.
I googled about the issue and saw that the original game could actually corrupt saves itself, I couldn't find anything regarding Flycast specifically to know if there's anything I can do to avoid it in the future.
At that point and also considering the QOL changes and additional content, as well as not caring that much about the reduced audio quality everyone agrees about, I switched to playing Legends on Dolphin and eventually reached the same part but I feel like the game kinda looks worse. Character textures seem more obviously low res and more importantly the draw distance in the sky overworld may be the same or better but there is a very clear and distracting line some distance ahead where things come into view. I feel on Dreamcast, even though objects seem to draw in less gradually and more per chunk or something, they did a better job of making things appear as if they come into view from a fog (without the additional area fog before the first arcwhale scene, that seemed more or less the same on both versions).
Or is this just me? Or is it a side effect of generally crisper visuals (I tend to play games at native settings this period, with CRT shaders on RA/Flycast but since I use stand alone Dolphin there's no equivalent that I've been able to find and use there)?