When you start off in Tokyo, anywhere you go to afterwards will seem to pale in comparison. Maybe not at first, but if you decide to stay in any place for a relatively long period of time, say 1year and above, you will find yourself missing Tokyo and what she has to offer - the convenience, the many attractions, even the noisy crowds.
That was how I felt when I visited Hakodate not too long ago. This was my 3rd visit, and I was quite familiar with the place. My Korean friend and I were talking about whether he would prefer to stay in Hakodate or Tokyo, and he agreed with me that if he were to stay for a long time, he would probably choose Tokyo over Hakodate.
For me, I guess if I were to stay in Japan, my answer would be the same. I would choose Tokyo over Hakodate, over Kyoto, over any other place in Japan even, simply because Tokyo is Tokyo. Maybe I am biased since Tokyo was the first place I visited, and I have been here for over 6 years. On the other hand, my Japanese friend who hails from Kagoshima also said that if he had to choose, he would remain in Tokyo after graduation instead of returning to his native prefecture. Our reasons might be different, but the appeal of Tokyo is undeniable.
~If Tokyo were a girl, I would propose to her immediately.~