I have had a coupld of 5mt subarus in the past and all of them have the same thing that you are mentioning. It takes a while to get used to the gear ratios, but the differance between 1st and 2nd are so different that it will cause a little hickup which some call hesitation. All of the research that I have done I have concluded that the cause is that the 1st gear is set for a lot of torque and then going to 2nd wthich has a lot less, so there will be a little jump. I learned that there is a little more play with the clutch. Once you learn the transistion, it will be smooth as driving a 4mt.
Just my .02 worth