I really appreciate your comments.
After knowing how you think about my issue, I realized that 1 year is not a very bad. I will be more patient until I get the 3 years.
This year I paid the resident taxes and my sponsor did as well. So, next time we will submit all the documents showing that my family is having a stable financial life. Even in case they give me 1 year again, I will try to cope with the situation until I get a full time job with a good salary to make them have no doubts that I am not going to be a burden on their shoulders. It seems that I am not lucky enough with the immigration office. I asked my colleague at work from a South American country, she said that she knows many other people married to Japanese nationals and they still get 1 year extension every time.
I don't think it's a nice idea to change my current visa status to a student visa. The only reason is that if I am on a student visa, I won't be able to apply for the PR. The latter is the reason behind all the hassle man. As long as I know that 3 years visa will be sooner or later, I would wait for it. Also, keeping changing the visa status from marriage to student or working visa is not good thing for the immigration office. It may look suspicious to them.
As most of you have mentioned, my only choice is to be patient. I am currently doing a part time job and paying the resident taxes.
Next time documents will be:
1- Proof that I paid my both Κζ―Εands―Ε plus ΎΕB
2- Proof that my sponsor did as well.
3- Proof of my annual income.
4- Certificate of Passing the JLPT N2 and JLPT 1.
5- Proof that shows that I have been going to school that is why I could not do a full time job.
Note, even if I am doing a part time job, I do pay the health insurance for my wife and myself.
This is a link from the immigration office official webstie that shows what matters most to them:
http://www.immi-moj.go.jp/english/tetuduki/kanri/shyorui/Table3-2.html.
Thank you so much for all your comments.