To summarize the response, the person regrets that you can't be hired, especially because of the current job situation where even Japanese graduates have a hard time finding jobs. The chances are lower for foreign and Filipino engineers.
Your youth is an advantage in finding a job, but it is not possible with only JLPT 3. He recommends that you study hard and pass at least JLPT 1.
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You're having problems understanding because a letter of refusal is usually very polite and indirect--something that happens in English, too.
What this person writes is very true. Jobs are scarce, and a lot of Japanese fresh out of university can't find jobs. Tougher still for high school graduates. With the intense competition for jobs, employers aren't going to choose a foreign national over a Japanese who understands the language and culture natively. If you want to be hired in Japan, you need something exceptional you can offer employers--outstanding skill in some field (engineering in your case, I assume) and near-native competence in Japanese (reading, writing, speaking and listening).