My "impossible mod" would be a physics engine for the game. Where if you destroy the trunk of a tree, the rest of it falls down and becomes a heap of debris.
On the "doable but lots of work" list:
And a different aiming system, where kneeling behind an obstacle with only your head poking out makes you harder to hit than standing in the open, by having hits be centered relative to the total area of the target, but with more spread, instead of the current mechanic.
And an ability for units to "trample" terrain/units. Draw the route as if there were no obstruction, every step, apply (a ruleset defined) damage to any blocking terrain or unit (for a certain TU cost). If destroyed, continue, if still standing, stop. This would allow for reapers to burst through some walls, and tanks/sectopod to not be blocked by bushes.