To which you've provided very few examples of, to be fair. If you're saying "Portal" series then, sure, that's some brilliant, amazing work!
I'm not going to defend our story here, those who love it and get it truly adore it. You can find plot holes in nearly anything, from Lord of the Rings to Dark Knight. Story, like any art, can be somewhat subjective and is easy to pick on.
The GAF crowd can be somewhat cynical. If you go to Youtube and look up many of the cutscenes deemed "silly" or "cheesy" on here the majority of the comments over there cite how the scenes moved them, made them misty eyed, or out and out made them cry. And those of you citing Cole as some bad stereotype - guys, that's just Lester being Lester. We introduced Jace as a more laid back character as a contrast Cole's enthusiasm. (which, after playing his sequence, is his way of overcompensating for not being the center of the universe and having to risk his neck for a can of beans now along with some aches and pains.)
I believe we're getting better at storytelling with each effort and the critical consensus is that this is the best Gears narrative yet, and we'll keep doing better in the future. You can pick anything to shreds on the internet because you've got the time and balls afforded to you by a keyboard and monitor.
EDIT: And no, we're not going to answer everything. Creatives often leave certain questions unanswered so they can answer them later or let the hive mind of the internet to figure it out. The Gearspedia has already solved a lot of these questions.