You're right, and I'm having a hard time expressing why it still strikes me as extremely repetitive. I guess it's a combination of the intrusive UI, the overt display of the content structure (as in everything being numbered, named and distinctly categorized), and the copy-paste nature of the actual objectives. If they don't show me all that stuff up front, it's much easier to maintain the suspension of disbelief.
It's the reward structure and the lack of quicksaves for me.
The game heavily emphasizes the stealth/takedown aspect by rewarding you with exorbitant amounts of experience. Going in guns blazing will NEVER be as effective as focusing on takedowns. Takedowns and stealth also take much more effort, which means if you fail without hitting a checkpoint, you're going back and doing everything all over again. It also means that if you botch a stealth maneuver, you're effectively pigeonholed into going guns blazing. Every encounter is basically like that; the general design idea is that you'll be forced into an exciting gunfight once in a while, which leads to unexpected behaviors, but in reality this happens so often it's just annoying (YMMV here... some people may find this fun). Meanwhile, you're not really getting anything for hunting. There's no experience gain, and taking down big game isn't really a challenge because all you need to do is throw a grenade. If I were to design the hunting system, I'd make explosive weapons completely destroy the hide. Bullet weapons would heavily damage it, decreasing its worth. And if you kill it solely with a knife/bow, you get 2-3x the amount you'd get from killing it with a bullet weapon. Same goes for XP. But again, because you're not getting XP from it, and the gold gain from selling hides is paltry, the sole purpose most animals serve is crafting your first few basic upgrades. Past that, they're annoyances.
I don't think FC3 is a bad game at all. But there's nothing really grabbing me and telling me to play more. I find that I'll generally continue if I succeed, but as soon as I die I'll Alt+F4 and go play something else. Again, I chalk that up to the uninteresting story.