Apples and Oranges.
It's not all apples and oranges, Yakuza 3 is technically on a better level than Valkyria Chronicles and Yakuza 2 or Yakuza PSP is better than Valkyria Chronicles 2. The only thing you have going is the filter, which can still be achieved with high detail models.
Then you have the characters, Gunthar is not actually very interesting main lead compared to Kazuma and then look at the level of character development from the Yakuza games and compare it to Valkyria Chronicles. The storyline and characters are easily better in the Yakuza title, did you ever think playing through Valkyria Chronicles what a magnificent storyline it had? I very much doubt it.
I'll admit, music could one point many will not agree on but these tracks from Yakuza 3;
http://www.youtube.com/watch?v=HrCuSyuCDrIhttp://www.youtube.com/watch?v=9WBzFoYwSVYhttp://www.youtube.com/watch?v=uts6LH7WUYUhttp://www.youtube.com/watch?v=Qa65zMlDcL0Out do most of Valkyria Chronicles soundtrack for me. Infact, unlike other major SEGA RPGs, I cannot think of one standout song from that game, unlike with Phantasy Star 4 with Requiem for Lutz or Demon Breath from Shining Force or even the final boss music from Skies of Arcadia.
Then lastly you arrive on gameplay and it really does depend on what you prefer more.
I'm not saying Valkyria Chronicles is a terrible product or anything, but it's not an amazing product that outdoes everything is several other game companies do, it has it's flows too.