What I'd change to the Portuguese

For the land unique unit, I would replace the organ gun some explorer-like dismounted unit that would act like a gunpowder skirmisher (that costs gold, though), and call them bandeirantes or something. Give them a minimum range and an attack of like 8 with bonus vs archers just like skirmishers. Alternatively, some cheap crossbow unit based on the crossbow militia that existed in medieval Portugal.

I'd then do some sort of house nerf, like making them cost 30% more, reflecting the small dimensions of the country, maybe give a bonus to early infantry but capping the militia line at long swordsmen, reflecting how early Portuguese history featured a lot of small-scale assaults at castles, so encouraging infantry raids, but not allowing this to snowball into a strong imperial age infantry civilisation, where the focus should be more on gold units. Good early game small raid potential but becoming a slower civ in late game. Another possible change could be for skirmishers to have +2 bonus damage vs cavalry but no elite upgrade, reminiscing the Battle of Aljubarrota in which a largely irregular and unmounted Portuguese army beat a knight-heavy Castilian force double the size by making use of ditches, spikes and defensive formations, yet not allowing the civ to have strong trash in the late game.