Steven DeKnight, the director of Uprising, has been answering fan questions on Twitter over the past few days.
He acknowledges that Mako's death wasn't as dramatic or sad as it could have been. Apparently she was more important to the story in the original cut, but the studio removed a lot of those scenes, which makes her death feel more pointless. It sounds like the director shares this complaint with the fans.
Mako was supposed to have been injured by radiation during the end of the first film, which explains why she gave up piloting.
There was also supposed to be more dialog explaining the Kaiju's plan. Apparently the Pacific Ocean is the only place Kaiju can come through, hence why they don't just open a portal above the volcano.