I would have to disagree. Having been in a war myself, what I can say is that wars are very different based on your role. If you are in the trenches, I would agree, the Paizo system would be clunky and hard.
However, special operatives as part of a war would be amazing. You could be spies, with a propensity for wet work. Not necessarily assassinations (although that could be an option), but more of dealing with protecting hidden bases (caves, whatever), invading secret research/headquarters dungeons, protecting from assassination attempts (and you don't have to protect a dragon, you could protect an important politician who is siding with the dragons), etc, etc etc. The way you set it up for flavor, is that you work for the dragon in the beginning, and there is no war as you level to lets say 6 or so, and then you become their favored operative, the war starts, and due to attrition and experience, you become the elite forces by lvl 12.
The big battles could be part of the flavor. That is not what you directly interact with, but you are just hearing about it, etc. They would be there to set up the drama. You could even be partially involved in some, where you attack a flank and disrupt formations, etc. The options are huge without actually doing a 15,000 foot soldiers vs 10,000 foot soldiers and 300 heavy cavalry thing.
Maybe the final battle could be flying on your bonded dragons across a massive battlefield in order to get to a central magic ritual happening in the back of the opponents lines, such as several dragons putting together a ritual curse, etc. You then land, with battle swirling all around you, in a magically protected circle and engage in one last desperate battle for the end of the world. You could be separate from the rest of the battle by the circle, or you could set it up that every 2-3 turns, a random number of characters (1d4 lets say) enters your combat from both sides. You could even have a rule about how the battle is going that would shift one side or the other up or down from 1d4 to 1d4, or 1d6, etc, etc, etc.
To call it epic, would be an understatement. By this mechanism you would avoid constantly playing against dragons, ie always turning it up to 11, but get to have a vehicle where in one campaign 100s of pages of lore about dragons are written, and we learn more about them. And the end, would be just so amazing.
I know this is a very big bombastic kind of an ending. But thats me. One of the self written modules I played ended when we shoved all of our silver coins in a cannon that the DM put there for flavor and blunderbussed a horde of werewolves instead of running away. He had to rewrite the rest of the story.