This is my recommended order of missions for best narrative effect.
Cerberus station, Freedom's Progress, Normandy.
Normandy crash site. First thing the new Shepard would do is visit her old ship and collect the dog tags. Also a quick 200 XP.
Visit citadel. See Anderson, get reinstated (or not), do some side assignments for quick leveling.
Kasumi's recruitment. On the citadel: one dialogue to unlock Kasumi in squad.
Zaeed's recruitment. On Omega: one dialogue to unlock Zaeed in squad.
Mordin's recruitment. Go to Omega right away as suggested by Illusive Man. Bring Miranda and Jacob. Mordin will be useful story-wise and is a great squad member too.
Kasumi's loyalty. XP, 60k creds, tech upgrade, unlocks Flashbang Grenade, and you find the Locust, the best SMG in the game, crucial for all non-Soldier classes. Also check out the party dialogue for some hints on future missions.
Firewalker. Irrelevant story-wise, but 625 XP, 30k creds, and 10% biotic upgrade. Plus a cool Prothean sphere in Shep's cabin.
Garrus recruitment. Shep needs the old buddy. Mordin and Miranda for best powers; Mordin and Zaeed for best story (but too bad that Zaeed only has one line in a mission full of Blue Suns mercs).
Grunt recruitment. Garrus and Miranda for dual Overload against many shields. No mission-specific story dialogue.
Jack recruitment. Garrus and Miranda for dual Overload against lots of shields. Garrus also has some cool dialogue as a former cop.
Horizon. Mordin and Miranda. Important story-wise to have your leads, and Warp and Incendiary are useful against Scions and the Praetorian.
Lair of the Shadow Broker. This is often done later in the game, but: (1) if Liara was the ME1 love interest, Shep should go see her as soon as possible; (2) even if not, the Shadow Broker ship becomes a hub and source of upgrades, as well as the ability to retrain squad powers. Bring Miranda when you can, but Liara is your best squad mate here with her Singularity.
Tali recruitment. Miranda and Garrus for dual Overload against Geth shields.
Thane recruitment. Nothing story- or gameplay-wise. Bring who you like.
Samara recruitment. Nothing story- or gameplay-wise. Bring who you like.
One random mission so the game unlocks the next one. I usually do Miranda's loyalty at this stage. No particular squad member suggested.
Collector ship. Mordin and Miranda for a main story mission. Also Incendiary and Warp. Remember to pick up a weapon specialization or the Widow rifle. The latter is especially useful for Infiltrators: with the Cloak damage bonus, it can one-shot many mid-level enemies even on Insanity.
Loyalty missions as they unlock: Jacob, Mordin, Grunt, Tali, Garrus, Thane. Bring Grunt for Mordin's mission and Mordin for Grunt's. Bring Garrus for Tali's, best if with Area Overload. Other squads at your leisure.
Jack loyalty. Miranda for good Cerberus-specific dialogue. Need high paragon or renegade at the end if Miranda is loyal. If you screw it up, you may still fix it later.
Samara loyalty. Need high paragon or renegade to resist Morinth. At any rate, pick Samara at the end for better continuity through ME3.
Zaeed loyalty. Nothing story- or gameplay-wise. Bring who you like. If going the paragon route, you need a very high score to save the workers and keep Zaeed loyal, which is why this is best done as late as possible.
Derelict Reaper. Story-wise, Tali and Miranda have by far the best dialogue. Gameplay-wise, on Insanity you should bring someone who can deploy broad attacks with a level 4 power: Jacob with Pull, Tali with Attack Drone, Jack with Shockwave, Zaeed with Inferno Grenade, or Mordin with Cryo Blast. If you have Throw, be sure you have level 4 Throw Field, a lifesaver against husk hordes, particularly at the end.
Legion loyalty. Tali for obvious reasons. Also two AI Hacking is better than one! Two requirements: (1) delete the heretics; (2) keep both Tali and Legion loyal through a high paragon or renegade score. These are essential to the best outcomes in ME3.
LAUNCH THE SUICIDE MISSION RIGHT AFTER THE COLLECTOR ATTACK
Suicide mission. Your squad: Miranda and Mordin throughout, both for story and gameplay; Thane is a good option too, but he has no good lines. Second team leader: Garrus or Jacob. Tech specialist: Tali, Kasumi, or Legion. Biotic specialist: Samara or Jack. Escort: anyone, but it must be Mordin if you don't take him with you.
Overlord. Legion and Tali. Doesn't matter story-wise (except for one line about Legion), but these are best against geth anyway.
Arrival. Absolute last thing to do before Mass Effect 3. No squad mates.
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