This is the worst part of both campaigns in my opinion, with the well-cave battle being an easy second place. Some tips which have been pointed out in other threads on this topic, and which I've used myself:
Before starting Flames of Vengeance, if you are coming from the original campaign, take off your dragon armor (in dragon form of course) and save it. You can access your battletower in FoV so you could save it there if you want. Be sure to grab the armor before starting the FoV endgame though.
Once in the air at the start of the escort, pause the game and equip your armor. The game gives us default armor that lacks any kind of bonus, which is stupid, and this is why you should use your saved armor from earlier in the game. I prefer to use pieces that boost my offense so I can destroy things faster.
1. You gain a nuke skill on your action bar: use it by flying to the center of a fortified island and setting it off - this will wipe out all nearby structures. It has a long cooldown so use it carefully.
2. Summon your wyvern companion regularly to help keep enemy attention off of you.
3. Don't forget to heal yourself often; I usually did it whenever falling to 50% health in Casual mode.
4. Breathing fire seems to be more efficient than shooting fire spheres, but requires you to be next to your target. With practice you can shoot a fire sphere on the way to the target then finish it off with fire breath.
5. Try to stay well ahead of the escort zeppelin - this requires fast-paced play.
Some people have managed to wipe out everything - I maybe wiped out half of the stuff. I think this mission is the reason why I haven't bothered to play the game since. It really irritated me. I managed to do it on my third attempt, on Casual.
