Miranda and Garrus, and it isn't particularly close.
I like to be an infiltrator, and run with other people who can use sniper rifles. Garrus never got a rest, because he went with me everywhere (except for Mordin's recruitment mission). Aside from him, I shuffled around Zaeed and Thane, and Legion once recruited. As for my favorite female... anyone who's not Miranda.
Depends on the mission. In some missions you need people who are good in destroying shields in other against armor and so on.
Miranda and Garrus, and it isn't particularly close.
This. The only time both of them aren't with me are on loyalty missions, which is part of the reason I missed Garrus' "places that are fun to fight through" the first time I went after Maelon. I had Miranda with me.
Jack and Mordin.
On Insanity my priorities for squad mates usually focus on 1) defense stripping (highest priority), 2) AOE damage and/or immobilization, 3) squad ammo (early game), and 4) squad mate weapon damage (lowest priority). With that in mind:
Ladies: Miranda. With Overload and Warp she is incredibly versatile as a defense stripper, and can detonate warp bombs. On top of this her passive offers a squad bonus, and her useless loyalty power insures most XPs are spent on useful powers from the beginning instead of being banked for later. I also take Samara a lot mid-game onward (but usually with Miranda as opposed to instead of Miranda, since these two have great synergy). Kasumi sometimes on heavily shielded enemies.
Guys: This is much closer, and for me much more class and mission dependent. But Mordin is almost always high on list as he has AOE armor stripping and AOE immobilization (cryo) with 4.5 sec cool down, both available from early game. I often take Garrus when facing exclusively shielded enemies. Jacob early game for squad incendiary. Thane sometimes (in addition to Miranda) when I want to double-down on warp bombs (highly class dependent).
Miranda and Garrus were always the main squad members I used.
Sometimes I would swap one of them for Grunt or Tali but not very often.
Tali and Garrus. These 2 were my squadmates from ME1 all the way to the end of ME3
Miranda and Thane tend to do a lot of detonations and damage, especially to the collectors :3
Definately Miranda, she's versatile against enemies' defenses (overload shields, warp against armor and barriers) and her passive can boost your weapon damage (or health if you evolve it that way).
As for the second squadmate, I like Tali's and Legion's drone to distract enemies, but I like Grunt's pure (headbutting) strength as well.
Garrus is probably my favorite, personality-wise. Whether he's a LI in a playthrough or not, I love bringing him everywhere.
At the end I like Miranda and Thane. Thane has the Sniper rifle and Miranda I don't know what she does. Plus Miranda doesn't die in the end? But who's going to kill the husks for me? I'm playing on Veteran. Couldn't beat ArchAngel on Hard.
I'm not sure how you beat the game without a soldier since I've only finished with that on Veteran. And I also did an Adept on Casual.
Grunt + Jacob. Have never died once in ME2 even with other squad mates, but these two made the ride a lot smoother.
(what are games coming to these days - ME1 was a lot more challenging, died once in that game, still had a general sense of nervousness on ME1 missions)
Anyone that could use the Incisor sniper rifle was very strong (Garrus and Thane come to mind).
Miranda, Garrus, Samara, and Thane were my favorite for combat purposes. Shout out to Mordin too for heavy armor missions.
Grunt and Zaeed
Zaeed can do mid and long range support. Grunt has close range.
Particularly useful on my infitrator class. If we are dealing with a lot of long distance I have Zaeed in the back with me picking people off while Grunt acts as our body guard. If we have a lot of enemies that are comming towards us Zaeed with assault rifle damages them as they approch while Grunt finishes them off with his claymore. While I sit in the back picking off targets at will. Knowing I have 2 people keeping me safe while I snipe.
Jack is ok but I don't like about her attitude and her behavior. So, she's aggressive and powerful. I like Mordin too but not my favorite but he's awesome and cool. The one thing that I like about Mordin is he's very intelligent.
yeah that's one of hte main reasons why I don't get too involved with her. She's useful rfor taking enemies down with her biotics especially when you need a shockwave or 2 but beyond that I tend to stay away. I recently did her romance in my last playthrough but usually I stay away from her.
As for mine I've gotto go with Tali and Garrus but then those 2 and Liara are my favourite companions in the whole trilogy.
Male: Garrus, Thane, Grunt (in that order)
Female: n/a
I don't play with female squadmates unless there are no other options or it's required for the mission. They just hang out on the ship waiting/hoping to be romanced, while the bros go out and do the heavy work.
If Garrus is available, he's in my squad by rule. And that's throughout all 3 games. Sniper rifle and tech support.
Thane is my other favorite, but you don't get him until a little later in the game. So I use Grunt until then as a tank. Then swap him for Thane and go to an all sniper group of Shepard (Soldier), Garrus, and Thane.
Kasumi/Jack and Garrus.
Grunt, Thane and Samara were a "gold reserve".
Samara and Miranda. Because reasons.
Depends on the difficulty. Anything under insanity I like to take Tali and Garrus because I like them as characters and enjoy hearing their banter and want to see them besides my Shepard in the cutscenes.
Insanity though I swap out Garrus for Grunt. Tali and Grunt are a surprisingly effective combo in my experience. I remember her drone getting the attention of a bunch of husks that surrounded it and then Grunt just charged in laughing and punting them. It was pretty cool.
I have to ask about this though:
First of all, my favorite female squad member is: Samara. Why? Because of her cool powers and interesting personality but I really hate when Samara demands Shepard to follow the code without romancing Samara.
Next, my favorite male squad members is Thane Krios because he had very well-concerned personality about his son. He is very attractive but dangerous. I don't like the idea when Thane becomes a assassin. So I decide not to romance him because he is assassin.
When does Samara demand Shepard to follow the code? I've chatted with her many times in multiple playthroughs but never remember her ever demanding I follow a code. Infact she follows Shepard's code due to the oath.
Also what do you mean Thane becomes an assassin? He was already an assassin. Though I guess technically you could say he's "officially" retired in ME2.
Ashley and Liara. Ash is practically indestructible, Liara balances Ash with her biotics (ME1, ME3)
Miranda and Garrus in ME2 (Miranda is solid and like Liara on biotics, Garrus isn't as pathetically weak like he was in ME1 - it was a competition to see who needed reviving more often on a mission: Garrus or Tali in ME1).
On the suicide mission, Miranda and Grunt. On the human reaper, Miranda and Legion.
Female: Miranda, Tali, or Kasumi.
Male: Garrus, Legion, or Thane.
It's hard to choose. 
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