The Peninsular Campaign was the reason I got into Napoleon: Total War in the first place, but it was disheartening to see how half-hearted it was made.
Still, the Peninsular War would have some great options, like 4 different factions(French, British, Spanish and Portuguese). Each faction would have different pros and cons. It would fit very well with the prestige concept, and getting equipment/leaders/troops/money for prestige points. For the British, it may be better to get muskets to give to allies or guerrillas, while the Portuguese would want British leaders to bolster their army. The French would want supplies or counter-guerrilla efforts, while manpower would be expensive.
In addition, it would be cool to have horses as a limited commodity, and use of horses on all artillery batteries. Then you'd have to decide whether you'd get 12 lb'er guns, or stick with your 6 lb'er guns to save the number of horses used. The strategic choices would be extensive.