I'm not sure if the lack of a big impact of your choices is the real problem, because the ME series never really let your choices have much of an impact. Sure, it often implied that they would have an impact, but after ME2, who honestly expected your choices to matter all that much?
Lacking better examples, ME is nothing like Alpha Protocol or the Witcher when it comes to choices. ME as a series is like a Hollywood blockbuster in many ways, and if they had written the endings consistent with that, I suspect most fans wouldn't care that much about the lack of impact full choices. Instead, we got Casper and an attempt at being clever.
Checking out seems not to do much.