I guess you and I have different definitions of "nitpicking", as whether or not anything in ME can be defined as intellectual isn't entirely irrelevant for the topic at hand. Giving the franchise waaay too much credit is one of the recurring problems I see with people, ME devs and certain journalists included. It's not an artistic masterpiece like a Shakespeare play or a Rembrandt painting, and it's not intellectual, nor is it supposed to be. It's not Asimov, it's not 2001.
It's when you forget what you're making and try to get all deep and "intellectual" on the wrong basis is when you get a mess like ME3's final 10 minutes. So no, it's not nitpicking. It's the perception that space opera pulp can be called "intellectual" that's part of the problem these days.
If they'd accepted the franchise for what it is, they'd have followed up the "high level" choices with closure on the universe and characters they made us care about (and did a great job with it, no question), spiced with some actual variety derived from your choices. Instead we get a pretty simple, rehashed organics vs. synthetics thing we saw a million times before, add a cycle of extintion as a twist, and call the lack of closure on any of the characters or smaller concepts "intellectual". No, it's not nitpicking at all in my book. But I feel I've made my point clear by now, so I'm done here.