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.
According to an interview with one of the designers on Reddit, nearly half of the UNC missions were cut prior to release, with the number of visitable worlds originally intended to be double what it was in the final product.
Mass Effect 2
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).
There are emails and descriptions left over in the game code referencing unused missions, including one where The Illusive Man asks Shepard to retrieve several probes left on a planet in the Caleston Rift, a sidequest in the Citadel where Shepard could help a woman named Nara track down a mysterious stranger she met, and an additional objective during Tali's mission on the Alarei where the player would control a Quarian scientist who is fleeing to a lockdown room. Likewise, Captain Kirrahe was intended to send Shepard an email after the latter recruited Mordin, but this was also deleted.
It was possible at one point to have gay and lesbian love interests, but these were removed from the final product. Tali, for example, was going to be a potential lesbian romantic interest, but her voice actress wasn't comfortable with it and the idea was dropped.
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.
The Human Reaper apparently had a planned section where Shepard would use turrets to damage it. This was scrapped, but there is dialog in the voice files that has all of the squadmates telling Shepard to man a turret and destroy a certain part.
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.
Mass Effect 3
Many 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):
The leaked script had descriptions of many aborted/unused/changed missions, including:
Shepard was originally intended to have a trial (over what happened in the Arrival DLC from ME2) during the prologue of the game. The trial is interrupted by the appearance of the Reapers, forcing Shepard and Anderson to secure contact with the Normandy (much like the final game)
At least one mission had Shepard and a team assist in the evacuation of Palaven.
The mission on Eden Prime was originally intended to be completely different and completely integral to the plot, instead of just optional DLC. Shepard and his/her team would go to Eden Prime, where they would discover a statue that was made in Shepard's honor and talk to residents who are in awe of the commander. You also meet up with either Ashley or Kaidan's (depending on who survived Virmire) Spectre partner, who aids you in the mission against Cerberus' forces trying to capture Javik. Javik's purpose was completely different - when the team finds him, he is revealed standing in a crater surrounded by dead Cerberus agents, and would have had some exposition about the Crucible at the Catalyst. Later on, Shepard finds the Virmire Survivor's Spectre partner holding a gun on Javik (simply called "The Prothean" in this script), and Shepard has to choose between convincing him to stand down or killing him to save the Prothean. As a result of the mission (and Shepard being framed for civilian casualties by Cerberus), Udina strips Shepard of their Spectre status.
In light of the Eden Prime mission, Thessia played out completely differently as well. Javik would be an essential squad mate; he would communicate with the Prothean AI, who would reveal that the Crucible is the Catalyst, as in the final version. At this point, Kai Leng would show up, accompanied by, of all people, the Virmire Survivor, who had been tricked by Udina into believing Shepard was working with Cerberus after Eden Prime and that Kai Leng was an Alliance agent. You would either have to talk the survivor down, or kill them in combat alongside Kai Leng. There was also some script found about being forced to choose between saving Liara or the Virmire Survivor after the battle once the temple started falling apart, though nothing further in the leaked script elaborated on this.
Continuing from that, the Cerberus Coup originally played out completely differently and at a completely different point in the plot. It would occur after Cerberus captures the Prothean AI on Thessia and discover they need the Citadel to harness the Crucible and thus control the Reapers. Instead of being alerted and fleeing, the council would have been in session on an emergency meeting to determine whether or not they should abandon the hanar homeworld to the Reapers. There would have been no appearance from Kai Leng while the salarian councilor hid, and a final confrontation that would have included Udina trying to shoot the Salarian councillor and Thane taking a bullet for her, and Thane and/or Shepard killing Udina after he shoots another bullet that either grazes or severely injures the councilor. Likewise, in the post-mission scene at Huerta Memorial with Thane and Kolyat, Shepard could speak to the Council and rally their support in a much more apparent fashion. It would end with Shepard being awarded control over all of the other commanders in the Citadel Fleet. Kasumi would have also made a brief cameo in this mission if she survived the second game.
Thane originally had his own personal mission. He would ask Shepard to investigate a portable indoctrination device, which was stolen by Cerberus and tested on Kolyat, who resisted the device's effects and hid after his captors were preoccupied. Shepard would investigate the location where Kolyat was being held (a mansion), rescue him and discover a doctor named Dwait, who tried to indoctrinate Shepard (to no effect whatsoever).
The mission to recruit the Blood Pack was greatly changed from the final product. Shepard originally had to secure a breeding world for the mercenaries, and the only feasible planet had an existing research facility located on the surface. The player could choose one of several options, including evacuating the station, letting a third party sponsor evacuate the site (which would net War Assets) or just let the mercenaries kill the inhabitants. The mission got far enough along that a full set of dialogue options were written for it.
The Omega subplot would have been fully integrated into the game, and not just DLC. It 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 results in 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.
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.
Likewise, Wong had much more to do in the early script - if Allers was transferred off the ship, she would go to serve on another Alliance frigate but would be killed during a Reaper attack, and Wong would deliver a news report announcing her death.
Kelly originally had much more dialogue with Shepard explaining how she came to be in Cerberus' employ. Shepard could either accept her love or tell her that he's having a relationship. With James Vega.
The GX12 Thermal Pipe sidequest was originally part of a larger subplot that dealt with a Cerberus saboteur onboard the Normandy. There were plans to have one of the engineers go into the drive core and attempt to repair a sabotage attempt, potentially dying in the process. In the end, the sidequest was never scripted or animated, although plot flags for all of the engineers (potentially including Tali) are present in the game files.
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).
The Ardat-Yakshi mission originally had Shepard and their team being sent in to secure Falere and Rila, not because the monastery was being invaded by the Reapers, but because Falere and Rila were the ones turning the Asari into Banshees. During the mission, Shepard would have had to construct a makeshift staircase to proceed. At the end of the mission, instead of detonating a bomb, Rila feeds on a Banshee and tells Shepard and the others to run as she holds the rest of her turned friends at bay.
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 rescue the downed shuttle crew) and an alternate Conduit run sequence where Liara and Garrus get blown off their feet as they attempt to run from Harbinger's beam (which had its concept restored in the Extended Cut).
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.
The amount of content that was cut from or changed for the final mission, Priority: Earth, is staggering:
While the Geth Prime appears in the Alliance base before Shepard goes on the final assault (though only if the Quarians were destroyed), there were originally plans to have a Quarian representative as well, with both leaders speaking about their peace with the other side and their resolve to help humanity.
Several characters (including Grunt, Jack, Jacob and Zaeed, possibly among others) had dialogue related to killing Reaper forces on Earth, and many of them having further conversations, like Jack speaking to her students and Zaeed gloating over a dying Reaper. Likewise, Jack and Jacob had in-combat dialogue (albeit reused from ME2) present in the game files as well.
Text files from the early script indicate that there were plans to have the mission function similarly to the Collector Base mission from the previous game, with Shepard being told by Anderson to pick what fleets/ships will attack key areas.
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.
Also during the run, it was intended that Shepard's squad (as shown in the deleted scenes of The Final Hours of Mass Effect 3 and this reconstructed scene) could be blown away by Harbinger's beam, based on whether the player had high or low EMS. It was scrapped on the basis that potentially killing off two of Shepard's squadmates with no buildup or impact whatsoever was too much for the player. It was eventually restored in the Extended Cut, though with variations for high-EMS/low-EMS and a different sequence of events.
The events leading up to the final confrontation with The Illusive Man had more clarification over what the Reapers were doing on the Citadel, with various processing stations set up that were converting its inhabitants (much like the previous game), and Shepard and Anderson drawing their guns on each other (due to TIM's influence) when they reach the control panel.
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. Another unused early concept◊ for the final area had only a single platform leading to the center of the room, and several Reapers were floating outside the Citadel watching Shepard's decision.
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.