So what's a better game, Ninja Gaiden or Bioshock Infinite?
See how pointless that is? The ONLY things the games really share in common are a Sandbox Style Environment and a first person perspective.
But ok whatever I'll bite.
Not only is Farcry not a better 'rpg', it's an inferior game in general.
1. Side missions+ mini games in FC3 are a boring, uninspired afterthought.
2. The FC3 sandbox environment while beautiful, is incredibly shallow. Once you kill a tiger for the umpteenth time and realise you are taking out the same outpost again and again, shit gets old fast. And don't even get me started on the laughable NPC character model and voice variety.
3. Complete disconnect between what you are doing in the main narrative and the random crap you get into in the regular game world. Almost to the point that it's like playing 2 separate games: One is some Call of Duty style spectacle on-rails shooter while the second is some kind of first person Just Cause 2.
4. Characters. While Skyrim's characters weren't particularly memorable or that well developed, it at least makes up for it in variety. My big gripe with FC3's characters, is that everyone goes on and on about how awesome they were without actually looking past the cool voice acting.
Look at Vaas for example. All you ever really learn about him, is that he's a nut case drug addict who wants to kill you because someone told him to. That's it. Then he disappears from the story. We never learn anything of his real motivations, past, personal experiences etc. He's just 'cool bad guy' stereotype. Same can be said for nearly all the characters in the game.
5. Exploration and rewards. In skyrim, I explore a cave and potentially find a nest of bandits with traps and treasure. In FC3 I explore a cave and find copy+past 'chests' with nonsensical vendor junk and maybe some lame ass collectible that I'm collecting...just because.
And let's not forget the modding scene, which adds immeasurable depth to Skyrim that FC3 could never hope to compete with.