Yes, anti-magic field is going to cancel out any spell that has a duration other than "instantaneous" - ie, enemy caster casts Poison on you, you fail your save - you step into an anti-magic field. You are still poisoned, because the magic duration was instantaneous, the spell created the poison you are afflicted with, but once the spell ends, you are still poisoned because that is a mundane effect, and not a magical effect.
Certain Arcane casters are built to take advantage of Transformation, especially ones which take the prestige classes Eldritch Knight and Dragon Disciple. It can also be useful against opponents who are immune to the caster's spells entirely, such as certain constructs. Transformation would be used at the end of a long self-buff routine.