The betaversion of the game featured a number of elements that were not included in the final product, including a different default character model for the male Shepard (before they brought Mark Vanderloo on to provide the face-capture model), a different voice actress for Ashley, different default armor for Garrus (who also does not wear a visor over his left eye in this version) and a completely different Galaxy Map. Notably, however, it also gave the player the ability to play as your squadmates (and make Shepard a computer-controlled ally), and the combat interface was much more intricate and involved than what eventually appeared in the final version.
Furthermore, the planet Therum is called Caleston in this version and rather than search for Liara as in the final version Shepard and his squad is instead attempting to rescue a colony of miners.
At one point in the original game's development, it was planned (and uncovered, via a file in the PC version) that the player could save Ashley and Kaidan during the Virmire mission, with both of them commenting in a cutscene afterwards about a "stunt" Shepard pulled to get them out safely. Both characters can be modded into later missions (including the endgame at the Citadel), but they can't both be imported into the sequel, as the game locks up when the player meets them at Horizon. This was cut on the basis that no-one would ever import a save with just one of them and it would complicate future plots.
According to Mark Meer (the voice of male Shepard), the Turians were going to make clicking noises when they talked. The dev team scrapped it because they believed it would be distracting.
Mass Effect 2 had several gameplay elements and sequences deleted from the game before its release. By hacking the PC version, it's possible to discover deleted files and voice-overs that reference these deleted elements. Chief among them was the ability to go for any of the recruitment missions at any time after you received the Normandy SR2 (including Legion, who only shows up in the final game on the mission just before the endgame begins).
It was possible at one point to have gay and lesbian love interests, but these were removed from the final product.
At one point, Mordin would have had the option to create a biotic field (during the "Long Walk" portion of the suicide mission). Several voice files were recorded with Mordin telling the team he can create a biotic field, and his reactions during that section of the mission. This also implies that he would have had biotic abilities, whereas in the released version he is a pure tech specialist.
Deleted voice files indicate that there would have been a confrontation scene between Mordin and Grunt. This was removed to focus on confrontations between possible love interests (Tali, Miranda, and Jack).
Originally, Kasumi and Zaeed had very different loyalty missions. Kasumi's involved stopping a corporation planning to use bioweapons against the Alliance, and Zaeed would have involved killing a fellow bounty hunter who had gone corporate, and then faking Zaeed's death.
Harbinger originally had a longer ending speech as Shepard and his/her team flee the Collector base, where he comments that many more Reapers will be coming soon. It is believed that Shepard's dialogue in the worst possible ending, where s/he falls from the Normandy, references this deleted footage.
It was possible at one point to complete Tali's loyalty mission without ever seeing the body of her father, Rael'Zorah, and have others comment on the fact that he couldn't be found.
Originally, Liara would have had her own subplot about getting revenge on the Shadow Broker. This was later realized in the Lair of the Shadow Broker DLC.
Several plotlines and missions were cut from Mass Effect 3, including a large amount of material that was part of an early script for the game (which leaked in November 2011):
A much longer and much more involved Priority: Earth mission, according to the leaked script and deleted audio files found on-disc. Several characters (including Grunt, Jack, Jacob and Zaeed, possibly among others) had dialogue related to killing Reaper forces on Earth, while the push to the Conduit was severely stripped down from its original idea. Depending on the player's EMS (in the script), Joker could swoop in with the Normandy and blow a hole in the Reaper lines, and Shepard would make a run for the Conduit. The resulting scenes would have either depicted Shepard entering the Conduit just as Anderson is attacked by a husk, both of them entering the beam together (and both being severely injured) or the final ending where Shepard gets up alone, bloody and bruised before making his/her way towards the Conduit.
The leaked script had several descriptions of aborted/unused missions, including:
The Omega DLC originally began as a more complex series of missions that involved Shepard returning to Omega (which is being blockaded by an Admiral Armitage instead) and sabotaging Cerberus' operations by heavily bombing their flagship during a boarding run. This would have opened up Omega as a secondary mission hub, complete with more vendors and missions. Furthermore, this extended mission chain would make players gather supplies for the station, as well as travel beyond the Omega-4 Relay again to stop Cerberus' activities and look for a destroyed frigate in the ship graveyard that was carrying a valuable treasure. In the end, Shepard would come face to face with Armitage's enforcer - Zaeed Massani, who could either be reasoned with, bought out, wounded or killed outright.
Furthermore, text files in the Omega DLC itself indicate more elements that were planned but never implemented: a sequence where Shepard and Aria search for items in the maintenance area (along with a reference to the activation of the fans in the "Mordin Acquisition" mission of the previous game if a save was imported), a much larger final battle (where Shepard has to protect Aria from swarms of troops as she destroys the power sources keeping Petrovsky safe in his control room), a different death scene for Nyreen Kandros and conversations regarding the whereabouts of Patriarch, Ruck and the "Biotic God" Volus.
A set of missions where a terrorist attack at the Citadel leaves dozens of casualties, and Commander Bailey puts every Hanar into an internment camp for security measures. Shepard then discovers that the Reapers have set up a base in the Hanar systems, and must stop it. This had a follow-up mission where you would travel with Kasumi (if she survived the previous game) to the planet, and unless the player saved the Graybox in 2, she would die during the mission. This was streamlined for the final game.
At least one mission where Shepard and a team would assist in the evacuation of Palaven.
Javik's recruitment mission (and purpose) was entirely different. While the team found him on Eden Prime, he has a completely different entrance (he is revealed standing in a crater surrounded by dead Cerberus agents), and it is revealed that he's The Catalyst. Later on, Shepard finds Ashley/Kaidan holding a gun on Javik (simply called "The Prothean" in this script), and Shepard has to choose between convincing them to stand down or killing them to save the Prothean. This was later repurposed into the "From Ashes" DLC (sans the Spectre plotline/V.S. confrontation).
A mission where you would escort reporters Khalisah Al-Jilani and Emily Wong (who was alive in the script) into the Citadel Wards to question witnesses and catch footage of Cerberus atrocities, ensuring that no one on the Citadel would ever work with Cerberus again.
There was originally planned to be an extra quest with Admiral Xen onboard the Citadel if the Quarians survived the Rannoch missions. She would email Shepard asking for Spectre authorization to experiment on Geth platforms (which were either dead platforms if you destroyed the Geth, or from stolen Geth if you made peace). If permitted, she started developing suicidal AI bombers that would upload a virus before destroying its target. Eventually, Xen would fly off the handle and start experimenting on the Citadel itself, forcing Shepard to go in and either kill her or force her to surrender (which then leads to her going to work on the Crucible).
A plotline where Kai Leng convinced the Virmire Survivor to work with him. Later on, at Thessia, Shepard is injured after a piece of rebar gets impaled in his/her side, and s/he has to choose between saving Liara or the VS (who are both in danger at the same time).
The "Final Hours of Mass Effect 3" mobile app shows several deleted scenes, including a longer conversation with the defense committee, an alternate Earth escape sequence (where a shuttle full of Alliance marines take out the Husks attacking Shepard and Anderson, who are still surrounded) and an alternate Conduit run sequence where Liara and Garrus get blown off their feet as they attempt to run from Harbinger's beam).
Notably the extended Earth escape features the injured gunship pilots being rescued by the Normandy's shuttle in the background, fixing a minor plot hole.
The Conduit run scene was restored in the Extended Cut for those players with a low-EMS.
The "Art of Mass Effect 3" book shows that the Illusive Man was originally intended to be the final boss of the trilogy - he would transform into a Reaper-fied creature, and Shepard would have had to fight him. This was scrapped as TIM was a Non-Action Big Bad who relied on his intelligence rather than physical ability and thus seemed too "videogamey".
Drew Karpyshyn's original idea for the third game's ending involved "Dark Energy", which was foreshadowed in Tali's recruitment mission during 2 and hinted at in the Arrival DLC. The game originally ended with a choice for Shepard to destroy the Reapers (and let the galaxy fend for itself against the "tech singularity", which would arrive sometime in the far future), or allow the Reapers to assimilate humanity in an "ends justify the means" scenario.note Neither Karpyshyn nor Bioware has confirmed whether this is legit.
At one point, the final room with the Catalyst/Guardian was intended to look like a garden - there were originally ghostly trees present in the perimeter of the room, and these textures can still be found in the game code.
There were supposedly plans at one point to make the multiplayer similar to Team Fortress 2, as a large number of textures for what appear to be either joke items or item pickups, including crates for different classes and Christmas presents, are still located in the files.
There was originally going to be a spin-off multiplayer game called Mass Effect Team Battles, which was to be played from first-person and involve several players beating cooperative missions together. This was scrapped, and eventually merged into Mass Effect 3 as its multiplayer component, though the perspective and gameplay was shifted to better resemble traditional Mass Effect combat.