Well to me, I thought the story of Symphonia was overall better, because Vesperia's lack focus and the main villains are pretty generic or, in Duke's case, too underdeveloped, while Mithos is someone you get acquainted with early enough and get tidbits of background for as you continue your journey through the other world. I also really liked the plot twists in Symphonia, I didn't really seem them coming yet when I think back on it, they did such a great job foreshadowing them or hinting at some of the twists, while Vesperia's plot twists were mostly just "wait, why?" to me, like Alexei being the great mastermind just didn't make sense overall.

In terms of dungeons, Symphonia's certainly felt like it had more variety, but tbh I didn't really like most of the puzzles and found quite a few of them more annoying than fun (the Darkness dungeon puzzle in particular was really bad due to how stupid the dark blob AI could be), and think I overall would take the few simple ones in Vesperia over Symphonia's.

In terms of combat, I kinda disliked the lack of free run in Symphonia, and though Lloyd felt more varied in moves, I overall liked Vesperia's combat more as it felt polished, more "free" and overall more enjoyable to me personally, but I think this one is more a personal preference thing.

For characters, I personally thought the Symphonia cast was rather bland outside of a few (Kratos, Mithos, Zelos). Vesperia had it's fair share of bland and boring characters too (I thought Judith was just meh) but I also adored the relationship and characters in it more (like Estella/Rita, Estelle/Yuri, Yuri/Flynn) and found myself caring more about the overall cast in Vesperia than Symphonia. And tbh, I wasn't really a big fan of Lloyd or Colette, Lloyd struck me as too idealistic/naive and Colette was rather too "sweet and clumsy" for my preference, while I enjoyed Yuri and his vigilante style, and Estelle and her journey to understand herself better.

I also liked the skits in Vesperia more, idk maybe it was just me but I didn't find many skits funny in Symphonia, while Vesperia had so many that I enjoyed, while they also did a great job playing off the groups dynamic and personalities.

If I were to give an overall idea of what I thought Symphonia did better, it would be story, foreshadowing, plot twists, dungeons and villains.