Everyone's experiences and opinions about Tokyo are going to differ depending on what you're looking for/what you're doing there/the resources you have/the people you know, etc.
Without letting any of the praise or bashing get to you, the best way would be of course to visit a range of areas in Japan, if you have the resources to do so that is.
So yeah, there's definitely nothing wrong with visiting Tokyo first, as long as you keep Nyororin's and many others' words in mind that Tokyo doesn't equal Japan. And from the looks of it, you seem to understand that well enough.
And so I hope you enjoy Tokyo, because I absolutely loved it. Unfortunately, I can't help out with the housing situation since I'll be in a dorm, but good luck!