While I'm still playing through Far Cry 1, so I can't compare to 2, I loved the feeling of stealth in that game. It was actually somewhat difficult, yet rewarding. Enemies could actually spot you at a reasonable distance instead of being completely blind. It made sense because you red shirt would stick out against the green foliage.
I read somewhere that the MP5 was crap until I picked it up and realized it was silenced and had a single fire function while remaining one of the most accurate weapons in the game. Spotting a patrol of four or five guys walking down the road towards you, hiding, waiting for them to get close, then silently killing them all in an ambush with a quick series of headshots. Omaigawd, it's so fucking amazing.
Or using the sniper rifle to draw people to one area while sneaking around. I shot a sniper out of a tower. The whole area moved into the area I was while I moved into their fort, stole the explosives I needed, and got out with nobody noticing I was there.