Some ideas I saw that I think are the best changes/additions:

*Stage 2 Overhaul
(faster, more rounded asteroids, and a glowing radius of where they will hit)
*Stage 5: Antlion Invasion
(they can come from the ground in random places)
*Stage 6: Madness
(elite soldiers, hunters, and antlion guards spawn)
*Destructible Buildings
*AI Nodes
*Start Invasion Manually

All ideas above are from these people below:
Level 4 Sentry
T1NYT4NK
Gazzer

Now for my additions/changes to the existing ideas:

*Stage 6: Madness
(Elite Soldiers replace Combine Soldiers)
(Hunters replace Shotgun Soldiers)
(Antlion Guards replace Antlions)
(Poison Zombies have a chance to replace a Fast Zombie)

*AI Nodes
(Navmesh should be included since it is different)

*Start Invasion Manually
(I would like to select which Stage happens and which ones don't)