The problem with rolling them into the unit is that outside the division level, they aren't handled in combined arms style. If you take a look at the structure of one of the United States' divisions*, the air component is its own separate brigade within the division. Once the rest of the division is translated to Trans-Newtonian terms, the air units would probably fall into the Assault Infantry category, but that's not really elegant. Many other nations don't integrate their air forces at all with their ground troops. (Also on the elegance side of things, including the attached aerial brigade brings every American division to five brigades, and Aurora only supports four. Stripping off the air units was a handy way of dealing with that. )
The second problem is handling Air Forces, since these really can't be rolled into an Army's divisional strength in any sort of accurate fashion.
I hadn't thought about having some form of leap in anti-air technology that no one has managed to beat by building a better aircraft yet, but that is a possibility to think about.
You could start each faction with Airfield PDCs and conventional-drive fighters. Heh.
Water navies are obsolete when you can hop to the other side of the world in seconds. Submarines might still work but would be slooooooow on a TN combat scale.
I had considered that option as well, TheDeadlyShoe, but while I'm crazy enough to research and write fairly accurate counts and names for the military of every nation in the world (Working on #12, The Philippines), the idea of trying to fight a massive air war between hundreds of fighters at once makes me cringe a little.
At least initially, no one will have the ability to hop from one side of the world to the other - my idea is a fairly slow conventional start, and moving a division across the world will take a bit longer then seconds, though that will be represented in the story rather then Aurora.
As an aside, if anyone knows of a good free site dealing with military strengths, organization and unit names that doesn't want to charge large amounts of money to be accessed, please let me know. I figure Wikipedia is good enough for a semi-realistic game, but sometimes finding information is like pulling teeth, especially for more secretive nations like North Korea or China.
* An example is below.
hxxp: en. wikipedia. org/wiki/3rd_Infantry_Division_%28United_States%29#Current_structure