This is my recommended order of missions for best narrative effect. Powers recommendation are based on my preferred class (Infiltrator) and difficulty (Insanity), so obviously YMMV.
Earth, Mars, Citadel I
Priority: Eden Prime ("From Ashes" DLC). Very first thing to unlock Javik. It also makes good sense story-wise to follow the Prothean lead right away.
Priority: Palaven. James and Garrus. Excellent dialogue among soldiers, and you need Incinerate and Proximity Mine against the Brutes.
Grissom Academy. Doesn't matter story-wise. For powers, Liara (Singularity) and EDI (Energy Drain), both of which are indispensable in the insane atrium battle.
Priority: Sur'Kesh. Liara and Garrus even just for the Shadow Broker line! For best powers, Liara and Javik is a better team.
Tuchanka: Turian platoon. Garrus obviously; plus anyone else.
Tuchanka: bomb. Same as above.
Tuchanka: Cerberus base. Garrus and EDI for dual Overload/Energy Drain with all those shields and turrets.
Krogan team. Story-wise, anyone. Gameplay-wise, James for Incinerate and Liara for Warp (but she dies easily, so Garrus with Proximity Mine is a good alternative).
FINISH ALL OTHER ASSIGNMENTS AND CITADEL QUESTS
Priority: Tuchanka. Liara and Garrus for best dialogue inside the catacombs.
Priority: Citadel II. Garrus for C-Sec dialogue; plus anyone else.
Omega DLC. Story-wise, it makes sense for Aria to retake the station now, since Cerberus will be weaker post-Citadel. No squad mates, but Aria and Nyreen are exceptional. This is also a great way to level up, since there are dozens of med-kits.
Priority: Geth Dreadnought. Tali and Garrus for hilarious dialogue between them. You may want to retrain Shep's powers now for all the Geth missions.
Rannoch: Admiral Koris. Tali and EDI for a tech-heavy squad.
Rannoch: Geth squadrons. Anyone, since it ends up being a solo mission.
Shore Leave (Citadel DLC). If you're playing on PC and have both the Citadel DLC and the Citadel Mod, this makes the most sense here. It unlocks the Strip as a hub for the rest of the game: unwind at the bar, hang out with friends, and do the simulator trials for lots of good money and experience. The mod also allows you to play the mission but not the party, which may be done after the credits (optional). Some people like that as a way to wrap up the saga; others don't. That's up to you. If you're not playing on PC and/or you want to do the whole DLC at once, this is best left for the very end, right before the point of no return.
FINISH ALL OTHER ASSIGNMENTS AND CITADEL QUESTS
Priority: Rannoch. Tali and Garrus. Many guides exist to ensure Tali's survival and both the Quarians' and the Geth' support in the war. To be totally certain: (1) you must have resolved the Tali-Legion disagreement in ME2; (2) you must have deleted the heretics in ME2; (3) you must have done both the Rannoch missions in ME3; and (4) you must have a high paragon or renegade score.
Priority: Citadel III
Mesana: Distress Call. Liara best for story; also bring Ashley for good dialogue. It makes sense for an all-female squad (best with FemShep, of course).
Priority: Thessia. Liara and Javik for great story and dialogue. This is a mission where you miss out on a LOT if you don't bring exactly these two.
Leviathan. This is here is because if it's done before Thessia, Shep looks like an idiot when talking to the Prothean VI. But it also makes sense story-wise too: after the blow on Thessia, Shep should be desperate enough to want to follow this lead.
Priority: Horizon. James and Ashley for an all-human squad in a Cerberus-heavy mission. Pick up the Locust SMG.
FINISH ALL OTHER ASSIGNMENTS AND QUESTS IN THE GAME
Priority: Cerberus HQ. In addition to EDI, bring your love interest for best story. Anyone will do gameplay-wise, but make sure that either you or another squad member has Overload or Energy Drain to fight Kai Leng.
Priority: Earth. Ashley and James for an all-human squad to retake Earth.
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