I think that they really WERE enemies, at least much of the time. In 1805, Russia was an Austrian friend, but after getting spanked for helping them against Napoleon, they adopted a much more hostile attitude. As if it were Austria's fault that Napoleon was bloodthirsty.
They were frequently both an enemy and a friend of Prussia, depending on, well, more or less the phase of the moon (I exaggerate, but not much).
Prussia and Austria hated each other, but were eventually forced to get along to fight the French. But, that didn't happen until von Blucher came out of retirement (1813?).
Even Prussia and GB, for whom it is essential to be allies, were not exactly the best of friends. More of an "enemy of my enemy" kind of thing.
Bottom line: Historical relationships won't work for game purposes if one wants a more balanced game. But, if one wanted a HISTORICAL game, then, well gosh, Prussia and Austria are going to get their collective butts kicked for the first 6-8 years.
So, there really are more than one sets of national modifiers.
I suggest three strategies:
First, have the AI national mods be different depending on whether there is only one human player, or if there are more than one. Historical numbers work if there are, say, two players and five AIs.
Napoleon has to become a lesser leader, or France will crush all opposition through the game. It doesn't seem like much, but making Nappy a 5.4.6 leader has an ENORMOUS impact on the game. Instead of near automatic wins against most enemies, he becomes their equal. He still has higher morale and movement, but he is not the crushingly overpowering leader he is at 5.5.6.
Him becoming a 4.4.6 leader has a similar effect, but not quite as pronounced.
Third, impact the other major powers' decisions partially based upon how well they and their adversaries are doing. For this purpose, only victory points matters. I suggest something like a check done annually or quarterly, where the number changes downward slightly if the potential enemy scored more VP than the deciding nation did. Note that this change should only impact the numbers in one direction.
Finally, there's the ultimate non-change: Bid more. France should be able to defeat the AIs bidding as much as 100+ VP. Against humans his edge is a lot less, but still, 50 VP as a bid should be quite feasible. This is a built-in "handicap" that everybody is required to use. Of course, if everybody bids zero, ...
At LAST! The greatest campaign board game of all time is finally available for the PC. Can my old heart stand the strain?