What if there was an equipment that allowed small permanent walls to be built? This would allow for more strategic defense building. Each would only be half a mech tall, so two would provide full cover, but one would only provide a small advantage. There would be a limit of how many could be stacked so you couldn't have your flag or doors covered to the point where you can't jump through. A limited amount of walls would be provided, but you could recycle old ones, allowing for more freedom, yet preventing you from covering the entire floor and walls with them. Another measure against confusing gameplay could also be that walls can only be placed on your side of the map, as not to cause confusion of whose walls are whose. If an enemy runs into the opposing teams walls maybe a small amount of damage (think half of one full auto multicannon shot) would be applied. This way you can place them around corners as mini traps for speedy players who are not cautious. That would also add some more depth to the attackers side as now they need be aware of popular locations of walls.
Edit: They would not stop momentum as not to create anticlimactic stops in the middle of an intense flag run.
Preferably they would also be opaque, so they could act as visual cover as well.