I never played either and with baulders gate on sale for 5.99 and warhammer quest at 4.99, I want a new rpg for the ipad so which one?
I would recommend Baldur's Gate, but wouldn't actually buying a game for once just get in the way of you asking infinity billion questions about them?
Baulder's Gate is a no brainer in my opinion. It's on a time limited sale so get it while it's cheap. Baulder's Gate has a ton of content and is a PC RPG classic. Warhammer Quest is serviceable for what it is but easy and repeatative (you fight the same enemies in similar looking dungeons for 10 hours). Warhammer Quest is worth $4.99 but if you're short on cash then it's not essential, the application of board game rules is admirable and it's atmopsheric.
If you have access to a PC then forget BG on the iPad. I'd recommend Warhammer Quest because it's cheap and because the BG port isn't quite as good as I hoped it'd be.