Valkyria Chronicle is a far more polish and visually pleasing expirience with superior and innovative gameplay. The story is standard anime-bait but well executed with decent characterisation. There is very little flaw that you can pick with this game. Any fans of SRPG should give it a shot.
Disgaea 3 is a throw-back of the PS2 era with horrible in game animation, nice asthetic presentation and a large dose of humour that's hard to find anywhere else. The game can last you a LONG time, far longer than VC, but only if you find it's rather repetetive gameplay appealing enough. The mechanic is simple but also very addictive and can drag you in for hours if you're not careful.
I'd recommend VC overall but I don't think you'll be dissapointed in D3 if you like the genre.
