Save the Rachni Queen (despite what various people in the game say about the Rachni, the queen will be true to her word about not letting the rachni loose)
Don't kill Wrex (He plans to give the Krogan a more stable future as he is committed to curing the genophage and resolve all tension between the Krogans, Salarians and Turians. Convincing Wrex can be done in 3 ways. Don't recruit Garrus and Liara, aquire Wrex's family Armour by talking to him several times after missions and then actually granting his wishes or get your Paragon/Renegade points maxed out)
Save Major Kirrahe (To do this, listen to the radio chatter during the mission and help anyway you can. Check your assignments every now and again for anything involving helping his team out. There will be at least 4 areas in which you can do something to help his team. First hack the control panel, then shoot the satellite uplink tower, next take out the Geth drones and finally turn off the alarm but do not reroute the Geth. Doing these will save the Major. You can then see him again on the Normandy before you go onto another planet and you'll then see him again on Sur'Kesh in ME3. He will save the Salarian councillor if Thane isn't present or was not interacted with before the Cerberus coup but will die soon after. He can be acquired as a war asset if Thane saved the councillor. You may have to interact with Kirrahe in order for this to happen like you would with Thane. Not available in the PS3 series)
Opt to save Kaiden during the events on Virmire (While his and Ashley's roles in the rest of the series are similar, he is OK with being around aliens while Ashley will be more hostile and Kaiden has a biotic team in ME3 and Ashley has nothing)
Save the Council (Yes this does resolve in losing heavy casualties, but it will mean that Shepard cares for other species other than his own, getting the respect and trust he deserves from the council)
Have Anderson as the human councillor (Do this because Anderson will be able to offer his military skills to the council and will grant an audience with the council for Shepard in ME2. Udina will be the human councillor by default in ME3 as Anderson finds that there is no action in his role)
Complete all other missions before the IFF mission (this will lower the amount of casualties in the suicide mission. Its highly recommended that after the IFF mission, you activate Legion and talk to him twice to get his loyalty mission and then do his LM soon after. After the crew are abducted, go straight for the Omega 4 relay and do not do any other mission)
Gain the loyalty of all squad members (make sure your paragon and/or renegade are maxed out for this). This includes the DLC ones as well. (They will all prove to be useful if they are loyal and will greater their chances of surviving the suicide mission)
In Tali's loyalty mission, use the paragon or renegade options (if available) in the second part of the trial or talk to the two quarian that you saved in missions that involve Tali before her recruitment, before you enter the Geth ship. Then use the Rally Crowd option. (Doing these options will give her an admiral role in the next game and if you resolved her conflict with Legion, she will try to convince the quarian that working with the geth is the best way forward)
In Zaeed's loyalty mission, don't save the civilians. (This will mean that he survives his small mission in the next game which will allow you to get better war assets from the volus ambassador in ME3)
In Samara's loyalty mission, do at least two actions in the VIP club to get Morinth's attention. As you talk use Art, Travel and Music and pick the bottom left answers (failure to do so will stop the mission). If successful, she will take you to her apartment and just let Samara kill her to gain her loyalty. (Morinth is a very weak character in ME3 as all she does is appear as a Banshee and that's it. Samara on the other hand will do more)
In Thane's loyalty mission, don't lose track of the target. (in ME3, interact with Thane in the hospital on board the citadel and he will save the salarian councillor, but will die soon after)
In Mordin's loyalty mission, keep the data and don't kill Mealon. (Using that data will cure the genophage in ME3 if Wrex is around as well. Otherwise destroy the data).
In Miranda's loyalty mission, let her see her sister before ending the mission. (Only seems fair really)
In Jack's loyalty mission, allow her to revisit her past before blowing up the place. (Again, it only seems fair and we also see a more vulnerable side of her)
In Legion's loyalty mission, rewrite the heretics and don't destroy the geth. (Doing this will further grow the Quarian's trust for the Geth)
In Garrus's loyalty mission, allow him to kill his target. (this will allow him to continue doing what he does best, leading the Turians to war)
In Jacob's loyalty mission, have Cerberus/Alliance take all the people home. (Regardless of the outcome however, Jacob's father will die, knowing that he made a terrible mistake)
In the suicide mission, use Tali, Legion or Kasumi as the tech expert, Garrus, Jacob or Miranda commanding both attack squads, Jack or Samara (or her daughter) as the biotic expert, Mordin as the escort and pick one unloyal and loyal squad member for your squad in each stage. Everyone mentioned needs to be loyal in order for this to work and if you do it correctly, everyone should survive.
Have everyone survive the suicide mission (Everyone needs to be loyal, all ship upgrades and various other upgrades are needed and after the IFF is acquired, activate Legion and do his loyalty mission and nothing else)
While it will lower some of the amount of war assets that you can get, destroy the collector base. (this will limit the Illusive Man's efforts to finding a way to control the Reapers)
Fully Upgrade the Normandy (squad members will be able to give you some ideas about upgrades).
Complete all DLC content but save both brothers in Overlord (Having one brother join Grimmson Academy), Warn the Batarians about the destruction of the mass relay in Arrival (which will greater their trust towards Shepard in ME3), use all the resources available on the Shadow Broker's ship in Lair of the Shadow Broker (which will help greatly in the next game) and complete all fire walker missions.
Now for the big one.
In Jack's side mission, save all the students (might be wise to do a wide search of each area of Gimmson Academy and also have Jack loyal). (Timed)
In Samara's side mission, use the paragon interrupt before she commits suicide.
In Jacob's mission, reassure Gavin Archer (the sick scientist from Overlord) that his brother is alive and well.
In Miranda's mission, beforehand warn her about Kei Leng and grant her access to Alliance records. Then in the mission, use paragon or renegade options to allow her to kill her father and rescue her sister without them both being shot in the process.
Disarm the bomb on Tuchunka. (Timed)
Cure the Genophage to get the Turains and Krogan as war assets (This will result in Mordin's death and loss of the Dallatress's offer).
In the Citadel and some of the Normandy arguments, side with the more vulnerable person.
If Legion and Tali survived the suicide mission, both loyal, resolved their conflict and Tali wasn't exiled in ME2, use renegade or paragon options to get the geth and quarians as war assets. Also save the admiral and colony and hack the Geth server in the side missions beforehand.
When in side quests, choose the option to get allies instead of using violence.
Complete all side missions before going into the Priority missions. (they will be locked out otherwise)
In Grunt's mission, if you saved the original rachni queen, save her again and make sure that Grunt is loyal in the previous game. (He will die otherwise)
Complete Kasumi and Zaeed's missions before leaving the citadel to avoid glitches and to gain them as war assets (must be both loyal). Also in Zaeed's mission, use the paragon or renegade option to get the bombers and the location of the colony and then speak to Zaeed in the Refugee camp to gain him as a war asset.
If Thane or Kirrahe lived through the previous games, one of them will save the councillor during the citadel invasion if you interacted with one of them beforehand. The one who saves the councillor will die however shortly after (might be wise to have Thane loyal).
Scan all galaxies to gain assets. Avoid gaining Reaper awareness while doing this. Some galaxies that have missions in them, will not be scannable.
Complete all Citadel missions (Get Batarian support by using the paragon option at the end of the terminal mission involving the Batarians).
Do not let Dr. Chakwas and Kaiden/Ashley on the Normandy and have the Doctor serve on the hospital at the Citadel (and choose Dr. Michel for the Normandy instead) and Kaiden/Ashley accept Hackket's offer. Their strength as war assets aren't at an all time high so if you want them on the Normandy one last time, then you have the right to do so.
Complete all DLC content (find all Prothean data before awakening Javik in From Ashes).
Promote a multiplayer character to the Galaxy at War mission.
Complete all missions before attacking the Cerberus base (make sure that your effective military strength is above 4000 to gain success).
Once all that is done, just choose the Destroy ending to have Shepard survive.
Now these are the best decisions to make for the best ending possible and I know there are many other alternatives available but that's how I would do it ultimately. Please comment if you have other ideas for the best ending.
UPDATE: After doing some research, I found that it won't matter on what decisions you make as long as the multiplayer character is at a decent level that will make him/her have enough strength to go over 4000 in Effective Military Strength (if the EMS is low, then a lot of work is needed but if its high, then less work is needed).
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