The fact that you can get so horribly overpowered in the games after the second one is why i get so bored with them. Even after getting upgraded guns in Far Cry 2 you are not casually mowing down dozens with ease and you don't have those broken takedown moves that turn the game into a complete joke.
Not to mention the AI is way better and way more aggressive in the second game, specially on the higher difficulties. They will flank you, hide really well as soon they know you are using a sniper rifle, throw grenades if you in a confined space to flush you out and so on. And in general they are just way more aggressive, they will not let up. In the games after that the AI is completely braindead and has no sense of self-preservation.
It even has the same fast travel method as Morrowind, you use actual in-game buses that move towards specific locations. You don't click a location and just teleport there.
You can tell with Far Cry 3 Ubisoft was very jealous of Skyrim and Call of Duty, it's why that game is riddled with those game's horrendous design choices like one click fast travel to any location and a perk system.