Portugal, Spain, the Rhine, Italy, Naples and I guess Tyrol, Serbian rebels and Spanish guerillas in their own right if you want more minor factions. These'd be the main factions considering the game is set in 1809. Also Russia, Persians and the Ottomans if you want to represent the Russo-Persian and Russo-Turkish wars. Mainly Portugal though !!
IMO it would be pretty pointless to add nations that barely or didn't even fight in any conflicts during the game's time frame before one's that did, or add factions without a logically enemy for them to fight. I think a good work around would to be implement factions as conflicts instead of standalone factions if they didn't fight in the Peninsular War or the 5th War of the Coalition. So if Russia were added next, it would be logical to add Persia or the Ottoman Empire with them (actually I forgot about the Anglo-Russian War whoops), while if Austria was added, it could be added as a faction on its own as it fought France in the game's time period. Then again, people are impatient.
Edit: this actually seems pretty tedious please don't do this.