"Third run"? This game doesnt need new game plus, you can replay the stage after all. You can also use some new units for previous stages, as long as that stage let you choose your own units.
Free stage select would be nice.
I really want to use Team Trinity. ZEXIS may hate their guts and Celestial Being was happy to disown them and see them die, but they deserve a chance to be used. Poor guys... even if they were sociopaths, they deserved better.