Thing is that two groups are bickering over this (the loudest anyway) - the fanboys and the... well 'haters' I suppose you can call them. It makes it hard to gather the valid reasons why a lot seem disappointed by -an aspect- of the game, rather than the whole.
The ending...
It basicly goes against Bioware's usual open-styled "your choice affects the ending" approach. The ending in ME3 seemed more like the sort of thing that happened to Deus Ex: HR.
To elaborate (without spoilers in detail - but it will elaborate on a general level many spoilers in the final battle, so read on at your own risk!):
The choices you have made throughout the journey of ME3, the hours you have invested into the RPG aspect are basicly thrown over the shoulder... it turns into an Action/FPS-styled story once the final battle begins... all aspects of "choices have a consequence" are removed. There is 1 plan, 1 way, and 1 outcome, with no variations at any point during the final battle.
- The forces you have gathered? Their size is meaningless... it doesn't matter if you gathered everyone into a holy unity, or just the minimum requirement - there are no progression of how they are doing during your own struggle either, not a word or a sound.
- The companions you have gotten to know? Besides a 'final talk about everything', nothing happens beyond this point - no closure or elaboration on their fates in the ending... their existence vanishes completely, even though they physically still might be seen.
- Harbinger, although shown and spoken of, does not even have a single piece of dialogue, he is encountered once, but only in an interactive cutscene, unlike the ME1 styled Sovereign encounter or ME2 Human-Reaper. Although it is a minor thing... the build up in ME2, seems neglected. Or at its worst... irrelevant - we might as well just have said "There is this super reaper - he is their leader, he is called Harbinger - beware of him!"... since he adds nothing to the entirety of ME3 in any way.
- The choices in your past? They hold no meaning or alteration towards the ending, whatsoever... from the moment you saw the endings of ME2, there was no more transferable choice to the conclusion of ME3... save perhaps if you allowed Tali and Garrus to live or die, their physical presence, but nothing more.
- And the one that hurts the most... and makes me think of Deus Ex: HR - The '3 buttons' choice. Regardless of your efforts... of what you did right or wrong... It does not matter at all, you are presented with the same 3 choices, regardless of your actions, with no impact or variation from your actions in the past - No paths are open or closed to you, to take or not to take. You click a button, and the ending rolls, with essentially the same ending, but with different moral values/lessons to be learned.
Now... don't get me wrong - for what it is. It is a good lesson to be told, how war has nothing but sacrifice and tragedy. How we have been spoon-fed that lesson during the cause of the entire game as a good theme... but with variations and a lot of choices: I.e: who to support and who not to. "Do I sacrifice these people to save these?" and so on and so forth.
However the final mission presents you with an anti of all the other missions... there is 1 route, 1 course of action... and a lot of "Oh and this happened/has to happen now by the way Shepard"... a lot of plot convenience and deus ex machina being pulled, that was never hinted... noted or even mentioned/speculated about in the universe... it seemed jaringly off for what it was. An ending that could fit in any game... which is why it might be disappointing. It seems too "not Mass Effect" to be Mass Effect, more general mainstream ending. Too linear and detaching - where the rest of the game has empatized on tons of atachment and story... your personal story that you controlled.
An example could be... make the bad/good choice - have the fleet you have gathered take up the fight with the reapers... if you did well/did not do well, in gathering your forces - you would see them slowly win/lose the warfaring, varying depending on your choices. Give us the choice to screw up completely like in ME2... for pete's sake, -Shepard could lose- in ME2, making ME3 never happen - that is freedom of choice in an rpg with an open end. This was not. ME2 left you with a feeling of "the more you invest, the more payoff you get". However ME3 was a huge buildup to an anti-climax... which is unfortunate.
For everything else up until that point... is rather good - really good and touching. But you can't make it so open to people, then just strip it away and ask everyone to just "go with this one way of doing things", don't feed us appertizers that are largely varied and flavored, only to present the main course as 1 dish. A good tasting dish, but one dish for everyone to eat none the less... with no fillings, addings or pasture.
That's how objective and reasoning I can be on this... just finished the game. It just feels... wrong to not say that it feels rushed and breaking apart in the last hour or so. So out of place. So forced... it screws with the RPG aspect sadly, which is not the right step for a franchise that was about the rpg elements.