I've wanted something like this for a long time.
Like you say, the openness of FarCry 3 (although even FarCry, Crysis etc) lend themselves very well to sniping. So you'd think there would be a decent game out, alas, not.
Ghost Warrior - is ok, looks pretty but has a lot of problems you'd think would be resolved for a sniper game. There are set paths, the enemy AI knows were you are instantly, there are too many levels where you aren't a sniper.
Sniper Elite V2 suffers from exact same problems. The times you do get to snipe are good fun but it is just too linear with too many enclosed areas and magic AI.
Sniper Elite hasn't aged well, while the gameplay might be ok it looks worse and more brown than Quake. I don't know if there are any mods but I've never got past the first level. (Ends up on Steam for under £1 during sales).
I'm surprised Ghost Warrior is getting a sequel so I'm interested in what those levels will be like but I guess it will be more of the same which makes it a rubbish sniper game and a very mediocre FPS.
There are the odd epsiodes in a decent FPS but I guess it is deemed not popular enough for its own 'genre'.
Or get one of these.