Uncharted is a wierd game for me because it got easier towards the end. I only died 3 times facing the mercenaries (). I died a gazillion times fighting the early pirates though. Then the difficulty curve picked up again in the last 1/4, and finally I nearly choked my controller in the last level. Other people I spoke to have different experience (They think the mercs are tougher).in a courtyard when I came out of the underground
For me the combat excels when the waves of enemies come from opposite direction, when you cannot camp or retreat to a safe entrance where you only need to worry about occasional grenades. That's also when the game combat is most difficult, frequent relocation and cover taking becomes vital. For pirates, I remember the plane crush site like that, for mercenaries, the Church which was probably most difficult for me.
Otherwise (ignoring minigames and mixed platforming shooting), one can always abuse corner shooting without even taking cover explicitly.