The games have different emphasis and focus. The original Fallout games put more attention into storytelling, dialogue, humor, and writing than Fallout 3, resulting in a game that was clever and engaging. The new Fallout emphasized exploration and discovery more, rewarding players who wandered about the Wasteland.
They are both good in their own rights, and depending on the type of game you enjoy, can be very fun (I personally can forgive poor gameplay elements if the writing is good, so I am a bigger fan of the original Fallout and Fallout 2 versus the new Fallout 3).
In all honesty, despite being related, they really can't be compared to one another.