Fandom Nod: Silversun Strip in the CitadelDLC has several pairs of off-duty mercenaries and regular troops you can overhear conversations from. Virtually all of them gripe about annoyances and issues in the multiplayer.
An asari adept and an asari vanguard complain about other biotic-capable races. This includes the drell, pointing out how one of them seems to kick the air for no reason and steals grenades all the time, and humans, who toss singularities way too often.
An N7 Fury talks with an Alliance requisition officer, discussing the new gear she's supposed to get. The officer ends up delivering a Graal Spike Thrower VII, thermal clip packs, and strength enhancers - all useless to a light biotic class such as herself. Turns out the Random Number God-nature of the store is just a hilariously inept bureaucracy managing the supply chains.
Fury: You are the reason we are losing this war!
A 'veteran' Alliance soldier and engineer go on a nostalgia trip (reflecting the nature of the game back at release) and consequently complain about how all their allies have shiny new equipment and rather improbable combat tactics (which is what the game has become after a year). Their points of discussion include two N7 characters, the new Armiger Legion turians, and biotic volus.
Engineer: Or those N7 engineers, with their grenade pylons. Who needs that many grenades?
Soldier: I joined up with turians on this drop onto one of their colonies...you know what those crazy birds bust out? Jet boots! What kind of frontline soldier needs a pair of damn jet-boots? It's just showing off is what it is.
Another complaint from the Veteran Soldier is the unfairness of N7 Demolisher's strutting around like a Walking Armoury.
It's not just the multiplayer, either. Drunk! Tali references an infamous forum thread debating what her sweat would smell like (no, seriously, that happened). "It just smells like sweat! Why would you even ask that?" Shepard references Jack and Miranda shippers, and Joker finally has the nerve to ask how Kaidan gets his hair like that.
While scanning Bryson's office for clues the first time in "Leviathan", EDI performs an extranet search on the term "basilisk" for Shepard. Among her search results is a video game enemy that's getting called "overpowered" on forums because of its One-Hit KO attacks - a criticism often leveled at Banshees on the BioWare site.
The Catalyst has earned the nickname "Task Manager", because it gives you the option of controlling the Reapers, altering them, or deleting them. In other words CTRL+ALT+DELETE. He's also commonly referred to as Starchild.
Similarly, 'Space Magic' for the power of the Crucible.
"Marauder Shields" and "The Three Husketeers", the four enemies encountered on the way to the beam in London that wind up being the final enemies you fight in the whole series.
The krogan vanguard in multiplayer is the Murder Train.
The new "retrieval" objective is Pizza Delivery.
"Enforcement gauntlets"? Nooooo, the batarians use the Falcon Punch.
"There are two endings I wouldn't like for ME 3. One being a random GOD LIKE force that saves the Galaxy or another being that to defeat the Reapers, everyone has to become a primitivist and destroy the Relays, Citadel, etc. Both would make me pretty unhappy as those endings have been done to death."
—screwoffreg, a.k.a. "the Prophet".
On the Mass Effect 3 Multiplayer boards, there were various ideas being thrown around for defecting Reaper troops. When the Leviathan DLC emerged, the Leviathan became the most lore-friendly means of doing so. Come the Reckoning DLC, that's what happened with the Collector Adept, though most ideas had the defecting Reapers still be thralls of the Leviathan.
Pre-release press statements were that playing Multiplayer, and getting their War Asset multipliers, would not be a necessity for those who wished to get the Golden Ending. However, though most endings can be achieved without Multiplayer, there are not enough War Assets available in the game to unlock the highest-tier endings. Although the Extended Cut DLC fixed it, the issue remains that the initial promise was a lie.
Mac Walters, the lead writer, made a statement before release saying that the presence of the Rachni played a major role in the third game or even just in the final battle. In the actual game, the rachni appear in one side mission, and don't appear at all during the final battle or any other time. It should be noted that this statement was made after the game went gold.
In a rare positive example, BioWare initially claimed that the Extended Cut DLC would not be changing the endings, but instead expand and clarify them. While there was definitely a lot of that, it also changed a lot of the more contentious plot holes and most of the Sudden Downer Ending, such as damaging the mass relays instead of destroying them. Cue (most) fans rejoicing.
Trolling Creator: The creator tweets refusing to explain the ending and saying to wait for future announcements, therefore fueling speculation like the Indoctrination Theory or ending DLC, and keeping the fan outcry from burning out. Possibly the ending itself, which was expected to create "lots of speculation". The new 'Refusal' ending from the Extended Cut is even being out and out reviled by many as a troll ending (although some fans specifically requested it).
A Reaper-ized version of the Illusive Man was considered as the Final Boss, but rejected as uncharacteristic: the Illusive Man's strength is his mind, so making him a bullet sink would diminish him. Instead, he casually strolls in and neutralizes Shepard with Reapertech indoctrination abilities; to win, you have to Talk Him To Death - either by Driving Him To Suicide to save humanity from his mistakes, or Taunting Him into dropping his guard.
There were deleted scenes and ideas that would have made the end much more bearable, such as the Normandy performing an epic Gunship Rescue while Hammer makes the desperate dash for the Conduit while taking fire from Harbinger (which was ultimately put back in for the Extended Cut), and this conversation between Shepard and Anderson.
From the script leak: a few post-Rannoch mentions of Admiral Xen, including a direct confrontation and Hackett reporting a botched attempt to hack the geth after peace is declared. She wouldn't have succeeded, but it would have cost the geth a few ships.
Ditto: the Thessia mission might seem like a gut-punch as-is, but it could have included a choice between saving Ashley / Kaidan and Liara. It's unclear whether there would have been any way to avoid it (say, if you held you own against Kai Leng), but all that remains of that scene is the bit where the temple floor collapses beneath Shepard. There was also a bit with Leng framing Shepard for several murders on Eden Prime to turn Ash/Kaidan against them. An alternative version of the script indicates that after the recruitment of the Virmire Survivor was moved to the Cerberus Coup story arc, the choice would have been between Liara and whichever other squadmate you took with you to Thessia (as Liara was mandatory for that mission).
Unused dialogue shows that there was originally more to the final battle (or that at least Jack, Jacob, Zaeed and Grunt played more of a role).
Originally, the team with Shepard at the start of the run towards the beam would have died no matter what, when caught in one of Harbinger's beams. The scene was cut after it was decided that just killing two of Shepard's team with no fanfare & regardless of Shepard's choices to that point was too cold hearted, especially when you factor in that it could potentially include Shepard's love interest. This is worked back into the Extended Cut - if your EMS score is too low, you're treated to the sight of Harbinger disintegrating both your squadmates.
Datamining has uncovered a massive amount of cut material. Notably: Javik and Eden Prime originally had much larger roles in the story, the Cerberus coup arc went much differently (Kai Leng was nowhere in sight and Thane's death was much more heroic), and Thessia was going to have a Virmire-esque decision at the end to save a squadmate.
Other cut elements include: a proper romance scene with Kelly, Kal'Reegar and Emily Wong not dying offscreen but actually being present and meeting Shepard, a lengthy explanation of the preparations that went into the Cerberus Coup, at least twice the squad banter both in-mission and on-ship (mostly discussing plot points left unresolved by the final game), and while it wasn't designed as a second hub (a-la Citadel) as initially promised, Omega served as a source for several lengthy quest chains that included hunting down Cerberus officers, venturing beyond the Omega-4 relay and, if you did particularly well, breaking the Only Rule Of Omega.
As with the previous games, leftover voice over files (and one interview with Mark Meer) imply that at some point in development James Vega was not only supposed to be romanceable, but also to be available as a Love Interest for Shepards of both genders (though the CitadelDLC reintroduces this element for a female Shepard.) The same seems to have been planned for Tali (there are voice-overs for FemShep for scenes that only take place with a romanced Tali).