The manual tranny definitely gets better after a few thousand miles. I have almost 20k miles on my car now and I hardly notice any difficulty in the 1-2 shift. Of course, regularly driving in Washington, DC traffic helps with this a lot because the car gets a good chance to get nice and warm and the shifting routine goes something like this:

First, second, slam on the brakes, first, second, slam on the brakes, first, second, slam on the brakes, first, second, slam on the brakes, first, second, slam on the brakes, first, second, slam on the brakes, first, second, slam on the brakes.

Well, you get the picture...