As futile as this seems, as a lot of the purpose in this thread, both by OP and responders, seems to be stemming wholly from negativity, I'm game to wade in here with my two cents.
First off, I strongly disagree with the use of the verb 'to matter' in this scenario. Whether or not something 'matters' is completely subjective to the person considering it. You can see that clearly here in this thread. Some of you clearly felt that the choices 'mattered' because of the knowledge you have as the gamer and because of what you add to the narrative in your own imagination. Some, like Karaphrut and jtav, seem to get more out of the story because they bring more emotionally into it themselves, while others evaluate the experience on a more technical or, may I say, clinical level and find it lacking. Not going to say who is right or wrong, or which is a better method for approaching the game, but you are approaching the game in different ways and then berating one another for using different measuring sticks when evaluating your experience. It's like a nose shouting at an eye for liking how something looks when, to the nose, it smells bad. Its stupid, arguing over it is stupid, and I hope you'll forgive me for refraining from using the term of whether or not a choice 'mattered'. For the sake of this post, I'll discuss whether a choice had an impact on the experience or not.
Secondly, I'll only consider the core game and the EC in this post. As a matter of course, DLC is somewhat divorced from the core game, so its value to this discussion is limited.
As far as I see it, there's four ways that the choices were expected to have an impact. Firstly, they were expected to affect our overall experience throughout the game. Second, they were expected to impact the setting as a whole. Thirdly, it was expected that the choices would affect the core narrative of the games, and finally, they were expected to have at least some influence over the conclusion of the Reaper War. It seems as though Bioware approached each of these separately, which is sensible enough in a project this big.
The first goal was certainly achieved. Little snippets of flavour text, NPC attitudes towards Shepard and one another, and the reputation/morality bars all contribute to this in some fashion. Granted, there are some areas where it falls short (Mordin's sudden change of heart even if Shepard was fiercely pro-Genophage in ME2, the lack of a big confrontation between lovers that seemed to be built up pre-release, and Liara's over friendliness regardless of how you treated her in previous interactions)., but for the most part it was done well. A lot of choices are remembered and acknowledged in some way. It was nice to see Jenna and Conrad brought together like that, and there were more than a few instances of this kind of acknowledgement that the player had previous experience within the setting. Like many have said, ME3 had a lot of dialogue recorded for it, and you'll never hear even the majority of it on any one playthrough. However, while this is all well and good, it is just garnish. A hint of flavouring in something much larger.
The second goal is somewhat less concretely fulfilled. We certainly make choices that should shake the setting to its core. Issues of galactic scales are dealt with right before the player. Anyone invested in Shepard or the ME setting as a whole can well imagine how this will impact the Galaxy going forwards. However, that's where things start to ring a little hollow. The writers begin to rely too much on inference and player imagination to fill in the gaps, rather than showing scenes and situations that accurately reflect a significant change to the setting. Sure, we may get to see the Geth and Quarians talk immediately after the Rannoch Reaper is toast, but where do we see the significant change this kind of resolution will bring? There is little to no real demonstration of how Shepard's actions have wrought change in the setting that goes beyond his own personal space. The epilogue slides are a sliver of compromise on this issue, showing whether the Krogan go to war in the future and who ends up inhabiting Rannoch further down the line, but its very minimal. We do affect the setting, but never in such a way that we get to experience it. This could have been resolved in a number or ways, such as changes to the crowds inhabiting the Citadel to show once warring races either still at loggerheads or perhaps slowly coming to terms with one another, or maybe granting the player the Crucible as a quest hub where he can witness his growing War Assets combining, the fruits of his efforts across the series. Just a few small things that are more passive changes to the atmosphere than actual scenes we take an active role in. Perhaps there was a time constraint that prevented this.
The third point is arguably the one that would require the most work. A branching narrative is not an easy thing to develop. In the few cases where we see it work, its often only done very close to the end so that differences can be minimalized (think Revan's betrayal at the end of KOTOR), or close to the beginning, such as in games that require that you choose a faction, although even simply allowing the player to choose where to go first (such as which Star Maps to go after first in KOTOR or where to go first in the other two ME games) can greatly increase the impression of malleability in the narrative, even if it is only a facade. In ME3's case, the narrative is extremely linear, the focus being more on elaborate set pieces that necessitated being executed in a particular order. There isn't even the possibility of choosing which allies to pursue first, granting the player a sense of agency within the story. The few moments where it does feel like the story diverges significantly along different paths, the narrative snaps back onto the central plotline almost immediately afterwards, negating any sensation of varying possibilities (funnily enough, its almost always Cerberus that causes the plot to be dragged back onto the rails once more. looks like they're the villains in more ways than one!). In short, it seems as though Bioware are constantly wanting to show you the next big idea they thought would be cool, without actually realising that all they're doing is dragging you around by the nose.
The final point, the impact our choices have upon the endings themselves, is undeniably the worst executed of the four. Mostly thanks to the EMS system, which was implemented rather than showing assets in action, being rushed through a generic, grey grind on our way to the Conduit was not a fulfilling representation of all that we had achieved. The disjointed nature of the ending issue in relation to the previous hundred or so hours of gameplay further heightened this sensation of underachievement. And, as I have stated elsewhere, the introduction of the concept of inevitability at the apex of a series whose base gameplay mechanic was self-determination was complete and utter folly.
In the end, the game fell short for many with regards to following through on previous choices. I know that the choice-consequence mechanic was a big decider in my buying into the franchise. As I pointed out, the window-dressing acknowledgements of previous experiences was nice, but my priority was on the following three points, where I was sorely disappointed.
TL:DR- Bioware tried. For some, they succeeded. For others, this game will stand the test of time as the biggest let-down in their gaming lives.