Silverblade, the aliens will always concentrate fire on your strongest cannon or if all the same strength the closest cannon to them. As result with just a bunker and three cannons they'll attack the two on the front row first, damaging them. Then you upgrade the back cannon and they'll revert their attack to it, allowing the front ones to heal. Then upgrade one of the front ones and they'll revert their attack back to it allowing the back one to heal.
Apocalypse mode is definately beatable, if you use the right strategy it can actually be fairly easy until the last 2 or 3 waves. Build a bunker in the front row, and put three ion cannons in each green square. @silverblade I know it doesnt protect the cannon but enemies will concentrate fire on sectors with cannons, killing civilians. Upgrade to lvl three, get another bunker on front row and another 3 ion cannons. Then focus on economy, then missiles.