Only infiltrating brains can order anywhere on the map but they can not order within certain distance of any enemy brain. This mechanic will stop exploits like smashing other brains with drop crates.

You can hardly hit other brains with drop crates due to its inaccuracy. Also, all AI brains quickly dig down into the ground to protect themselves from danger, I recommend you do the same to avoid the accidental bullet

I was able to use drop crates to bomb my enemy 5 times in one campaign. They aren't THAT fast in digging down. What about rocklets with craploads of bombs? What about a a eocket with a load of units that could easily kill the brain due to where they wre dropped off?

The openness of the game is very exploitable, and probably wont be fixed. For example, you can just make a teleporter to the bottom of the map right outside your brain in your bunker. Instant win (or at least stalemate). Nothing is stopping me from doing it, but the game gets quite boring for me if I use those strategies, so I avoid them.