I've been playing Farcry 3, and it reminds me of a really common flaw that AAA games have these days.
The core gameplay mechanic is often brilliantly polished and very interesting, but then the devs attach all these weights to it that just drag it down.
Farcry 3, for example, has three layers of metagame popup and story missions that are actually more boring than the random encounters. Seriously! A game where the random encounters are more interesting than the scripted ones!
This is hardly specific to Farcry. Nearly every AAA game these days features fantastic core gameplay that gets gummed up by something. Final Fantasy 498, Sleeping Dogs, Dragon Age - all had fun mechanics and good world design, but bogged down by various factors. (If you loved Sleeping Dogs, I bet you were logged in.)
At first I thought this bogging down was on purpose, to sell DLC. But so many of these games are bogged down by their characters, plot, or pacing - nothing to do with DLC.
No, I think the core problem is that game design teams are very big these days.
So the "A" team designs the core gameplay content, and then the "B" team does the 8 million pieces of scripted content the story needs. Or perhaps it's the "A" team, but under heavy time pressure.
Whatever it is, the core mechanic is typically one or two gameplay loops, and that can be iterated and tested on tissue-paper testers and just in general polished until it shines. But the scripted content is not so easy - each piece is an individual production, and while it can be tested by Q&A, it's hard to do proper tissue-paper tests on it.
So the things that can't be properly tested end up being significantly worse than the core gameplay loop. In the case of Farcry 3, I actually think the game is made worse by the mission plots. Even the cutscenes and dialog seems bad in comparison to the basic fun of exploring a world and getting jumped by a tiger.
I don't really have an answer for this, but I do have some possible suggestions.
1) Cinematic testing. Bring in tissue-paper testers to just watch the cinematics in the game, or at least the animated storyboards. Maybe read out a plot synopsis. Ask the viewers their thoughts on the various characters, what the things they liked and disliked were. Once their complaints are all about the stuff that they don't see, you're golden.
2) Understand what your core gameplay is, and that scripted missions need to embrace that. Your scripted missions shouldn't be Prince of Persia when the rest of your game is wandering around an open wilderness. Your scripted missions shouldn't simply be the normal incidental missions with stringent fail conditions.
Instead, make your scripted missions the same kind of gameplay, but in an amazing situation. If your gameplay is about wandering around the wilderness, your scripted missions should be about wandering around somewhere amazing.
3) Tissue-test your scripted missions, even though it's a pain in the ass.