Here is how I solved the last mission:
Crawler, followed by a shield generator, followed by a second crawler. At the beginning you should have enough money to fully upgrade the first crawler (allowing you to 1-shot the weakest towers) and the shield generator, plus I think upgrade the second crawler once. Naturally you should upgrade the second one as soon as you can.
You should not loose a single unit. While you can definitely recover from a loss, it's a good sign you are not active enough with your abilities. Also fully levelled units are very, very expensive.
On my first run I had the following troop-setup: Dragon - Shield - Crawler - Crawler - Shield - Supply (levelled to give decoys), with most of them levelled once or twice by the end. While this setup worked, I felt it to be much harder and much more micro-management intensive, since the convoy is much longer and therefore requires more smokescreens, decoys and repairs (the big laser by the processor required 3 decoys to cross without losses, while with my other setup, 1 smokescreen and 1 repair usually were enough since the shield was much stronger).
- The basic towers should pose not much of a threat, especially in the first setup since you can one-shot them.
- An energizer should never get the chance to charge up your deployments. Luckily in the last level this is much easier than in the levels where it gets introduced. If you zoom out to the route-planning view, you can check for line of sights and plan your placements beforehand. Especially in the last mission I didn't bother and just called in airstrikes - one is enough and lets you do your thing freely.
- Hacker towers are annoying but no big deal. Stay out of the bubble and sprint in and out if you need to use an ability. Note that often the shot that deploys the bubble follows you. If you notice that fast enough you can run to a place where it won't get in the way. Remember, as long as you are in it and not your troops, no harm done.
- Behemoth/Stormray towers can be nasty. The former less so with my first setup, since the shields are much stronger, but Stormrays always can zap away all your shields in seconds, so decoys are needed. Try to place them behind the tower, so they waste time turning around. Also avoid placing them in range of towers you don't need to distract, they'll just help get the decoy removed faster. Be aware that if your troops are out of range of the towers but you aren't, the they might splash your troops by shooting you.
In the final bossfight, be careful not to bite off more than you can chew, let your troops circle somewhere where they'll be able to hit the boss while not being shot at by dozens of towers. One trick I used was to let my troops drive between the two "entry streets". You can hit two of the boss turrets while having few other towers shooting you.
Smoke screen works great against the turrets of the boss, while decoy is good against the lightning/splash damage towers, as long as you a careful not to place the decoy too close to your troops. Don't forget to drop aistrikes onto nasty towers aswell, they deal a lot of damage.
Also, don't be too afraid to let your commander get hit. He regenerates fast and if he looses all his health you only become unable to do anything for 3 seconds (though that can doom you if it happens at the wrong time). I abused this to let my troops circle somewhere safe, sprint in to airstrike a hacker tower,
die a painful death fall asleep for 3 seconds and sprint out again.
And last but not least remember you can reorder your troops during battle. The front unit has no shields? Switch places with the third one and save a repair. Shield does not reset if you move a unit, as long as it does not switch the shield generator.
I hope this has helped, if not please explain more clearly what kills you.