Given that player freedom is such a large factor in the Mass Effect trilogy, BioWare had to take into account the fact some characters might not survive to see the end of the series. In order to make the trilogy work, alternate NPCs can appear at certain points in the story to fill in for lost companions, and these alternate Mass Effect characters are often overlooked among the series' colorful cast.
Since each Mass Effect game's save file can be imported into the next entry, characters who die in one title stay dead for the rest. This is especially important to consider when looking at Mass Effect 2 (and was the main factor in the harsh criticism of ME3's ending, as many players considered it too restrictive compared to the rest of the games).
Mass Effect 2's story culminates in the "Suicide Mission," in which it's possible for nearly every character in Shepard's crew to die. As many of these characters have important story roles in Mass Effect 3, most of the alternates present in the series appear during the third game to fill the ME2 party members' essential slots.
Mass Effect Alternate Characters - Urdnot Wreav
During Shepard's confrontation with Wrex on Virmire near the end of Mass Effect 1, Wrex can be shot and killed by either Shepard or Ashley if players fail to talk him down. In that event, he will be replaced with Urdnot Wreav, his broodbrother. Wreav is more traditional than Wrex, prioritizing his own clan over the future of the Krogan race as a whole - a factor that can lead to some vastly different outcomes when it comes time to cure the genophage in Mass Effect 3.
Mass Effect Alternate Characters - Padok Wiks
If Mordin is killed during Mass Effect 2's suicide mission, the task of curing the genophage will instead fall to Padok Wiks. Wiks is encountered on the STG base at Sur'Kesh and accompanies Eve both through that mission and aboard the Normandy. His role is nearly identical to that of Mordin, and both share fairly similar values, meaning ME3's gameplay doesn't change very drastically in either scenario.
Mass Effect Alternate Characters - Admiral Xen
Admiral Xen is first encountered in Mass Effect 2 during Tali's loyalty mission, then returns in the third game to assist with the fight against the geth and, later on, during the final battle with the Reapers. If Tali is killed in Mass Effect 2's suicide mission, Xen will also take her place in assisting Shepard aboard the geth dreadnought. Unlike Tali, however, she won't join the player in combat throughout the level.
Mass Effect Alternate Characters - Morinth
Morinth is introduced during Samara's loyalty mission in Mass Effect 2, in which players are tasked with tracking her down and killing her. During the final confrontation, Shepard is given the choice to assist either Samara or Morinth in battle. Whoever is chosen will become Shepard's companion on the Normandy, while the other will die. However, aside from sending an email to Shepard in Mass Effect 3, Morinth has little involvement in the rest of the series if she replaces Samara. That, coupled with the fact that her presence on the ship arguably brings more risks than benefits, means most Mass Effect players likely pick Samara instead.