They did a lot right with this game, and they did a lot wrong. Riffing on religion is fine, pointing out that extremism is bad is good! But designing a game where you're not allowed to enjoy the game so you can instead watch a lackluster narrative? That's bad. And that really is the difference between this game and the rest.
All the big bads in the other games you despise. You love to despise them, even. You WANT to confront them, but with any of the Seeds you don't *want* to confront them, you want them to be put in an insane asylum so that they can get better. So that they can be treated for the obvious abuse they've experienced growing up.
This is not a game to be hated or loved. It's a game that exists. If it had been done better, it would have been worthy of the high scores it received. Also, I have a feeling that this game was based on true stories that happened here in the U.S. despite the claim that it's entirely fictional. Some of the things portrayed sound exactly like some events I've read about, as though it was a thought experiment to see what would have happened if the issues had been left to fester.
I think, in the end, a lot of the flak aimed at the story doesn't come from ripping on Christianity, (Though really, it more weighs on sects of the religion, such as Mormonism, which is far closer to what is being portrayed than outright Christianity.) since most Christians will be able to laugh and shrug it off because that's just not what you do if you're a Christian, but due to the fact that they delved too heavily into reality and didn't make this about the absurd adventures we've had in the past. That and because this is a main, cannon, Far Cry game, all other games MUST now take place after the end of the world. FC6 must now be in a post apocalyptic world. Settle in folks, it's going to be a trip. Unless, you know, they retcon the ending of FC5 because "Oh but muh profits!"
Now the DLCs? Hoo, those were some good bits of work! I'd almost say the game is worth it based on the DLCs, which, despite the cliche Mars storyline, was absurd and fun just as Far Cry was supposed to be.