Yakuza has better graphics (The majority of Valkyria Chronicles is not impressive) the better storyline (Valkyria Chronicles is actually pretty generic and simple) the better characters (With the exception of Rosie, I cannot think of any stand out characters from that game, now Yakuza has Majima, Kazuma, Karou, Goda, Fuma etc) and even better music (I cannot recall one track from Valkyria Chronicles that can match Grudge, Fly, Ogre has returned etc)
The only thing left is gameplay and that is subjective, as Yakuza is an adventure brawler RPG hybrid whilst Valkyria Chronicles is a SRPG.