Hello! I'm a Malaysian, going to attend Sophia University's Faculty of Liberal Arts in April. I'm not sure if I can help you, but I'll just tell my story.
I got accepted to both Waseda SILS and Sophia FLA, but chose the latter for two reasons. First is that the FLA offered me a better scholarship ( well, I applied for Sophia's scholarship while Waseda offered me ). Second is that my mom wanted me to study in Sophia. I was fine with either, for reasons I'll talk about later. My mom is Japanese, so she's familiar with the whole reputation-of-university-determines-your-job thing in Japan. According to her, there's a thing in Japan that says ‘Œcã’q (sou kei jouchi ) which refers to Waseda, Keio and Sophia. This means they are considered to be in the same tier, just below Tokyo University and probably Kyoto University? There's also MARCH, which refers to 5 universities in the tier below the 3. She also asked for the opinion of a few friends in Japan, and the majority said they would choose Sophia over Waseda, although both are prestigious in their view. So I hope this clears you up on whether Sophia is comparable to Keio and Waseda in terms of (local) prestige and reputation.
Now for Japanese universities being a joke, anyone who did a basic research on Japanese universities on a whole would have read that many times. But I have noticed that almost all, if not all, of those who said that is from the US. As for those from countries like Indonesia and Malaysia, there's a clear lack of opinion from them online. So how is it really? Truth is, I don't care. Education in Malaysia has been, unfortunately, largely a joke itself. Among my friends, anyone with ambition and/or financial capability is trying their best go overseas to study. Some of my high school friends are already studying in many countries including the US, UK, Australia, Germany, Taiwan, China, Singapore etc, with many joining them in the coming year after finishing their A-levels locally.
Got a little off-topic there, but in short, you are worried you won't get a good education in Japan, that your degree might be worthless and you might not be qualified for your dream job. I don't care that much about any of that. I've mostly been studying and learning anyway. If the classes and assignments are a joke, even better. I'll have more time to do my own study and research into topics I have actual interest in. I'm fairly confident that it should be better than education in my country. ( hard to be worse to be honest )
About job prospects. I can't help with this. I myself have no idea what I'm going to do in the future. I'm just living my life as it goes. Hopefully I won't get stuck doing slave labour-like office jobs in Japan. I guess whether a job in a UN organization is possible through studying in Sophia would largely depend on what you are going to study and what kind of job in what kind of UN organization you're trying to get into. Looking at the Career Stats page of Sophia's FLA website, I'm guessing most graduates go into slightly better slave labour-like jobs in more reputable companies. Well. Your call.
This got longer than I thought... Hope something in that wall of text helped you with something one way or the other. Feel free to ask any more questions through this thread or PM.
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