I would get the Zelda bundle. It would definitely be more expensive, but it comes with a custom-decorated Wii U pad that will hold its value better in the after market. (not to mention it just looks cool) The limited edition Nintendo consoles tend to resell for a much more stable price. The same will likely hold true for the Zelda bundle. The ZombieU bundle will only hold its value if you hang onto the original box. The hardware it comes with is just the standard black launch Wii U. And getting a copy of the Zombie U game with the bundle isn't worth much, as that game has been on sale for next to nothing several times. (it was available at GameStop for $10 over the holidays)
The inclusion of the Pro Controller is the big bonus for that package. But the Pro Controller is mainly only useful for multiplayer games. It doesn't particularly add anything to single-player experiences. You're better off using the standard Wii U pad for games like that. And Zombie U is more of a single-player experience anyhow.
If you can find a Zombie U bundle for a significantly cheaper price, I'd say go for it. Zombie U is a great game, and having the extra Pro Controller is a nice bonus, especially if you want to play some one-on-one fighting games for the system. But I wouldn't go out of my way otherwise.