If you're going to hop 2 subways, might as well head to Union Station. You're within walking distance or a really short cab from Little Tokyo. The hotels around there are a bit pricy, but there's decent Japanese food around there. You might as well get the full weeaboo experience.
There's nothing wrong with most of the Koreatown hotels, as long as you're near Western Ave. Vermont Ave. and eastwards can be a little rough. Korean BBQ is good eatin' too - Soot Bull Jeep and their mesquite grills are legendary. Yukari-sensei will gladly join you.