I've spent countless hours on both, but Budokai 3 easily. Dragon Universe was a much better single player experience than BT3's Dragon History, I'd even say Dragon Universe is the best single player story mode in any Dragon Ball fighting game.
And I love the Dragon Arena, spent so many hours going through those 100's of opponents, and leveling up my fighters they way I wanted to. Like, my Frieza, I only upgraded his health. I maxed that out, gives him like 7 bars of HP but I also had the Mecha Frieza capsule, so once defeated he's fully restored as Mecha-Frieza. My Frieza had like 14 bars of HP, he never lost but it would take ages to beat the opponents because he had base attack stats. After I maxed out his health, I went straight to defense. So much fun to have these RPG elements in being able to build your characters stats like that.
The gameplay is also just much better.