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Marvel Heroes 2015 Ultimate Leveling Guide (Story Mode)

Now that Story Mode is viable, you can get a max level character with all the bonus Power Points, Health and Spirit; and all bonus items collected (Boosts, Matrixes of Unbinding, etc.) at the fastest possible way. Legendary Quests are optional though suggested at certain levels.

Tips and observations!
Have this guide open in another device, like a laptop or tablet, it will save you several minutes of alt-tabbing/alt-shifting! Have a Level 25 Uru-Forged item ready (any type, it doesn't matter) and use Bridgand's Fortune on it when you reach Level 25, great buff to Spirit.
Try and get some Jewels of Yggdrasil ready since they're cheap and easy to stock. They're available in the Asgardian vendor after completing the Defend the Door event on Chapter 9's Lower Asgard.
Get one Mkraan Crystal Legendary and switch it to every new hero, more so if you're going to prestige several times.
Regardless of how you level, you should really do all the chapter 8 and 9 quests, they give a ton of extra XP that's good for omegas.

Achievement Tips
Enter to all the Treasure Rooms (Golden Portals) and open the chest, important for the Tomb Raider achievement.

Prologue (Optional)
This chapter is located in New York City.

1. Complete "Trouble at the Raft" quest
Go to the [RAFT - CELL BLOCK ALPHA] waypoint.
Complete the quest.
Notes: Grab the Living Laser Medal (+Spirit) since it's a great help for new heroes.

2. (Optional) Complete "Finishing up the job" quest for a little extra XP.

Chapter 1 (Level Range 1-10)
This chapter is located in Hell's Kitchen.

1. Complete "Tablet of Life and Time" quest (+Health)
Go to the [BLOOD ROSE NIGHTCLUB] waypoint.
Defeat Doctor Octopus and complete the quest.
Notes: As you might notice, I've skipped several quests since they're not worth the time for the little XP they give at starter levels. This is normal and will happen in several chapters, it's generally to save time.

Chapter 2 (Level Range 10-15)
This chapter is located in New Jersey.

1. Complete "The Taskmaster's Lesson" quest (+Rarity Boosts)
Go to the [TASKMASTER INSTITUTE] waypoint.
Defeat Taskmaster and complete the quest.
Reach Level 15 any way you want.
Notes: I suggest doing this chapter Side Quests since they give a guaranteed extra Eternity Splinter.

3. Complete "Pursuing the Hood" quest (+Power Points)
Go to the [CARGO FREIGHTER] waypoint.
Defeat The Hood and complete the quest.

Chapter 3 (Level Range 15-23)
This chapter is located in Madripoor.

1. Complete "The Eyes of S.H.I.E.L.D." quest
Go to [LOWTOWN] waypoint.
Speak with Yukio to get "The Muramasa Blade" quest and grab
the Muramasa part near her.
Complete the quest.
2. Complete "The Muramasa Blade" quest
Grab the other part of the Muramasa.
Complete the quest.
3. Complete "Snakes in the Grass" quest (+Spirit)
Go to the [BAMBOO FOREST] waypoint.
Search for "Poison Glade" portal, it's located to the East of the map.
Enter and complete the quest
Reach Level 23 any way you want.

Chapter 4 (Level Range 23-28)
This chapter is located in New York City.

1. Complete "Corruption in Blue" quest (3x Matrices of Unbinding)
Go to the [UPPER EAST SIDE] waypoint.
Near the waypoint (to the North West) locate the "Police Rooftop" portal and go there.
Defeat Bullseye and complete the quest.
Reach Level 28 any way you want.
Notes: Since you unlocked Legendary Quests, you may do those for faster leveling. Also, you can go the other chapter waypoints and do Side Quests for some bonus Eternity Shards.

3. Complete "The Kingpin Falls" quest (+Health)
Go to the [FISK TOWER] waypoint
Defeat Kingpin and complete the quest.

Chapter 5 (Level Range 28-33)
This chapter is located in Mutant Town and New York City.

Reach Level 33 any way you want.
* Notes: Remember to distribute your Omega points at Level 30.

2. Complete "Purification Crusade" quest
Go to the [MORLOCK UNDERGROUND] waypoint.
Go to the [OLD TRAINYARD] waypoint.
Defeat Juggernaut and complete the quest.

Chapter 6 (Level Range 33-38)
This chapter is located at Upstate New York.

Level any way you want until Level 38.
Notes: It's time to choose a Medallion now: Either Magneto Medallion (-20 Spirit Cost) or Mole Man Medallion (+2 Intelligence and 10% bonus XP) are both good for leveling. You can get a Magneto Medallion in the next step, and Mole Man Medallion in Midtown Patrol challenge.

2. Complete the quest "Stryker Under Siege" (+Spirit)
Go to the [COMMAND BUNKER] waypoint.
Defeat Magneto and complete the quest.

Chapter 7 (Level Range 38-46*)
This chapter is located in Savage Land.

1. Complete the "Infestation Most Vile" quest (+Power Points)
Go to the [S.H.I.E.L.D. SCIENCE STATION] waypoint.
Enter in the "S.H.I.E.L.D. Science Station" portal and complete
the quest. 2. Complete the "Mutate Genesis" quest (+Health)
Go to the [MUTATE MARSH] waypoint.
Locate "Evolution Facility" portal (it might take a while) and enter.
Complete the quest.

3. FREE TIME! (kinda)
Read the notes and reach Level 46.
Notes: Ok, this chapter is terrible in many ways and we're too far from the next one. Story artifacts are useless, except maybe Maht's Arrowhead if you're still lacking in Spirit.
Best thing you can do here is go to Industry City Patrol and farm items along with Legendary Quests. This way you will level up, and probably get some much needed Cosmic and Unique Items.
If you have a teleporter, feel free to do the other Story Mode quests, but don't try it if you don't.

4. Complete the "A Sinister's Plan" quest (+Spirit)
Go to the [SINISTER LAB] waypoint.
Defeat Mr. Sinister complete the quest.
* This chapter is badly tuned. Leveling is recommended until level 46 and then change to a new chapter.

Chapter 8 (Level Range 46-52*)
This chapter is located in Eastern Europe (including Latveria).

1. Complete all the Story quests in order
Complete "Starktech on the Loose" quest.
Complete "Defeat the Intelligencia" quest.
Complete "Smash HYDRA!" quest (+Spirit).
Complete "Victory Lap" quest.
Complete "Hulkbuster Armory" quest.
Complete "Poisoned Brew" quest.
Enter Castle Doom and complete "Doom's Lethal Legion" quest.
Reach Level 52 before the Doctor Doom fight.
Complete "A Doomed World" quest.
Notes: Important! Before going against Doctor Doom, make sure you level until at least level 52 - this will give you the Ultimate power you need to try and get the "X vs Doctor Doom" achievement.
This chapter is also the best time to pop any XP boosts since for an hour you will get tons of XP.

* Max level reached should be level 52-55, before switching to the next chapter.

Chapter 9 (Level Range 52-57*)
This chapter is located in Asgard.

1. Complete all the Story Quests in order
Go to the [FJORDS OF NORWAY] waypoint.
Locate the S.H.I.E.L.D. agent that starts the
"Mysterious Readings" quest.
Complete "Mysterious Readings" quest.
Go to the [ANCIENT RUIN SITE] waypoint.
Complete "A Frosty Reception" quest (+Power Points).
Go to the [LOWER ASGARD] waypoint.
Complete "City Under Siege" quest.
Complete "Throne of Deceit" quest (+Spirit).
Complete "Claim Your Reward" quest.
Notes: The remaining levels have to be done in any way you want - enjoy!

Chapter 10 (Level Range 57-60)
Notes: Chapter 10 has been confirmed but it's not in the game yet.

Source: http://steamcommunity.com/sharedfiles/filedetails/?id=493155455