I am going to go against the grain here and poop on two a little bit. Outside of the companion interactions, it really did not do much story wise. There was some propped up booheyman villian you never really interacted with (Collecters, Harbinger I think?) and a whole lot of "Shepherds dead, whatevs" in that game. Some of the companions were descent (Mordin, Thade, Legion) but some were just forgettable (Thief chick, Tattoo bitch, Grunt) or outright cringe (the Justicar woman, Cerebus Chick). At no point did it have something resembling the race against time feeling of the other two games, plus it suffered from the lack of the core characters from the first game (esp Liara, Wrex, and Tali). It did benefit from DLC a little and the end fight was at least unique. The Mission was laughable though, because you pretty much only had to make two correct calls the entire time for everyone to survive the suicide mission (contrast to Virmire where someone had to die) and the only real choice in the game was if you shit on Martin Sheen at the end or not, which ultimately had fuck all of an effect on the final game, regardless.
Three had flaws, to be sure. Super anime Ninja and the poor handling of the ending (mostly due to writer changing and forgetting their ME1 lore) stick out to people, but it also had a few pacing issues (We are saving the galaxy from a civ ending invasion, but lets go stop at the cititdel to shop). It also locked some of its best content behind DLC paywall. But the companions were on point (Tali suicide scene is one of the best written ones in the series) and choices as far back as ME1 impacted outcomes of relationships with them. The multiplayer was also honestly some of the most fun I have ever had in gaming and I am not someone who enjoys it normally. Its just a shame it took a patch and the Leviathan DLC to unfuck a lot of the garbage writing at the end.