Size: Santa Fe > Tucson
Price: Santa Fe = Tucson + $4,000
Engine: Santa Fe can have a V6 engine, Tucson no longer can (older models had V6).
MPG: Santa Fe is about 22/28, Tucson is about 25/32
Tucson also recently went through a model-redesign in 2010, so it's "brand spankin' new" the santa Fe model has been out since either 2006 or 2005. It's due for a model redesign soon, so what I'm saying is the Tucson will probably have more creature comforts until the refreshed Santa Fe comes out in the near future.
Both Hyundais, both reasonable vehicles, both good warranties, both small/medium SUVs, both can have AWD... drive each one, see which you like.