I have made a couple observations with stacking and the 3 in a Rows.
First of all, from what I can tell (and should answer RobT as to why not to go straight for 3 in a row), once you collect a 3 in a row, you can't start the others until you've completed the first level. If anyone has been able to get all three 3 in rows scoring at the same time, please let me know. Hopefully, this is something that will be addressed with a future code update.

That said, you can start two 3 in row lines at the same time, and is my current approach. I start with Destroy the Drill or Save the Enterprise, then Klingon & Space Jump, and finally Prime Directive which shows a cool graphic where the hand swipes over each of the rows on the display and then notifies you that Super Ramps and Super Pops are activated. I try to hold off on Klingon MB (or start my 2nd) upon completing the double 3 in a row, then use the opportunity to combo the ramps to double the super ramp values, while ball saves and black hold ball add work off my Super POPs. Also, as others have mentioned, I try to focus on combos, and have found that Nero can pay off huge if you can quickly combo the pink shots after the mode starts; I've had shot values during that mode in excess of 1.2Mil.

Has anyone completed levels 2 and 3? I'm curious if you start Kobayashi again, or if there are different modes. I'm also curious about 3 in Rows on each level, do the Super values increase exponentially, or do they values just increase based on mission progress?