I think it really depends on where you are planning to go. I reckon I could spend months in Japan without running out of things to see or do. It's an amazing country, especially if you get out of the cities. Beautiful mountains, skiing, but also beaches. And the food....
If you're going to do South East Asia though, I'd vote for KUL. MH fly to a lot of places in Malaysia and beyond and it's well located. The city doesn't have a huge amount to offer though. Hotels are cheap though; I was there a few years back and got a suite at the Hilton Sentral for the first of a basic hotel room in London. Hong Kong is great but it's quite a trek to most places in South East Asia.
Tokyo makes little sense to me unless you want to see Japan. But you should. It's also dead easy to navigate nowadays.