I wholeheartedly agree with the OP. One of my biggest complains concerning the trilogy is the lack of real weight to almost all the decisions the 3 games present: don't get me wrong there's weight to them, but they are so predictable that it's almost painful:
You are a renegade = cliche bad boy almost to the point of being a really stupid cartoon villain => you'll be punished for your evil deeds: no matter what you do the consequences of your ruthless or calculated deeds always lead to a greater evil. You are a paragon = nauseatingly typical hollywood/disney hero guy => all your ridiculously angelic deeds will be rewarded and lead to something absolutely rainbow tinted and great.
Yeah, the ending takes this away from people: thankfully, if you ask me. At least there's one really difficult decision in the whole trilogy which makes you uncomfortable and forces you to think twice. I'm not suprised though that so many are upset about the final moments, since it was made in a whole different spirit. Up until then you were pretty much in control of everything, while in the end you were in control of the decision but not of its consequences nor the circumstances. Which is great: I expected this from the whole trilogy. I never got it.
Which is funny since ME sometimes struggles really hard to be the dark sci-fi saga it aimed to be... but somehow it ended up somewhere half-way between the mature sci-fi adventure and the disney-star wars type of light hearted family entertainment space opera.
This predictable moral system and choices and consequences system is uninteresting in my opinion. The story does not dare to take risks and surprise the player. Like as it was created for little kids or teenagers exclusively. It tries to teach you morally instead of make you thrilled and be on edge, thinking hard when you make those decisions.
In my opinion there's no real sense in making a choices and consquences game if you make it this over-simplified and straight forward. The only thing you will get is a predictable good guy or bad guy story with all it's moral lessons: not thrill, no need for thinking, no surprises, no uncomfortable moments just a simple puppet show: my Shepard, my Shepard, my Shepard... blah, blah, blah. Hell even the side-characters do as you wish and love you no matter what. There's no sense of real tension or dynamics between the characters whatsoever (except for a very few cases).
The Witcher games in this regard are far superior. Thoses games are starring an already existing short story and novel protagonist, yet they give you more opportunity to role-play the character than ME which gives you a blank slate character which you define by his or her deeds or decisions. Well you do, but you do it way too much or over the top. Your decisions in ME do not only represent your control over your character, but also over the whole situation, consequences included. No surprise so many are so entitled to their so called "own Shepards" and their stories.
ME while a great game trilogy is only an action-adventure game with a very simple and predictable interactivity (c&c and moral) system - a powertrip for youngsters and some not so hardcore, but great entertainment for those who would prefer something intellectually and skill-wise more challenging. TW is a great and challenging action-RPG with a very well thought out moral and c&c system which makes you sweat many times and tend to challenge you a lot (in many ways). It's no powertrip and definitely not a fairy-tale for young people who look for their heroics-fix and predictable moral story.
I hope the next ME will be a lot more ambitious, challenging and mature in this regard.