Ignoring the differences is like ignoring the acting, dialog and artwork in a first person shooter because they're all just grabbing weapons, running around, and hitting the shoot button.
Farmville in its current iteration is designed to involve your facebook freinds at every level.
Its reward schedule is blatantly designed to encourage social sharing - basically making players skinner boxes for other players.
Tiny tower on the other hand can be played in entirely single player fashion, without really being bothered by "Oh you need 3 paint flecks to paint window X! 5 windows, 2 chairs, 4 cuboards, 2 cashiers left to open store! Ask your friends for parts"
Farmville is far more diabolical than tiny tower. Its obvious the tiny tower guys are more into making a game, while farmville is just plain sinister.