I don't know anything about what Tomb Raider has been doing to annoy people. But I do know a little bit about Resistance. In Resistance, you can quickly blast through the games from 1 through to 3 and feel reasonably satisfied with the story. But if you're one of those people who just wants more from the game's story, then after carefully analysing Intel and stuff, you can draw a bigger picture and gain a better understanding of the full picture. But one thing that stands out, are a lot of unanswered questions. I myself haven't touched Resistance in ages, so can't remember exactly what I'm talking about, but from memory they made the world of knowledge seem far larger than it was. By leaving a few things out for us to figure out on our own.
Especially around Russia, and the Cloven. We have all these nice contained little stories that could be leading onto the origins of them, but we never quite get there. Is this Insomniac's typical lazy storytelling? Did they really have no idea where they were going with these? Or did they just want to leave it open for us to never find out. It doesn't seem like them to be lazy around a story, but maybe they just didn't want us gaining a full picture? Maybe they wanted us to fit more closely into the shoes of whoever we were playing as. Do you think Hale or Capelli really knew (or even cared) about how the Cloven came to be, and why they worked in the strange ways that they do?
Then again that kinda contradicts what I use to think about Resistance, in that it was more centered around the Chimera then the soldier in which we controlled, by teasing us with the picture at the start of Resistance: Fall of Man. But that sort of crumbled with Capelli's crappy little story in Resistance 3 no one cared in the slightest about, because clearly we were all really pissed that Capelli was turned into a completely different character named 'Joe'.
I haven't talked about these games in a long time… sorry about that.
EDIT: That is a bold statement about that being the "best 3rd in any series"… I'm sure all the Metal Gear fans would be in an uproar hearing that line being used for a game that isn't the legendarily unbeatable 'Snake Eater'. I'm not though, because I don't like the intro song to that game… most overrated theme song ever!!