Right before the detonation of the large nuke, Mako said something to Stacker. It wasn't subtitled and I don't speak Japanese. What did she say?
She said 「せんせい あいしてます」(sensei aishitemasu), which means "I love you teacher/elder." This was confirmed on Twitter by Travis Beacham, Pacific Rim's screenwriter.
Mako Mori is a Japanese name, which was my first clue that she's Japanese. The others were that the language she and the Marshall spoke early on was Japanese, and the city in her flashback was adorned with signs that had Japanese, not Chinese, on them.