I say they bring back/expand upon some of the ranked-only missions. For example, levels of the battle sprite levels like the haunted railroad station, gremlin prison camp and sunset steppes. There should also be puzzle stages, bringing back starlight cradle, Trojan graveyards, and a munitions factory. Sorry this suggestion is super short, feel free to expand.
I'd love to see new puzzles, I've got the solutions for most of the current ones memorized.
The spotlights from the collector's mission that let rockets aim at you would be cool to see used more, and I'd love some kind of puzzle where you need to hit multiple switches at the same time with charge attacks or slow moving bullets.
I'd add some specific puzzle setup ideas, but that would be complicated and would give the solutions away.