Low%

Listed below are all the lowest% for the three prime games, and what is collected and skipped in each (updated from Kirby's pastebin)

Metroid Prime

Notes

• Item Loss Skip has been looked into a long time ago and won't really happen without some wrong warp. There are two item loss sequences: the visible one on the frigate (which is skippable), and the moment you land on tallon overworld. So even if the first one is skipped, you'll lose everything upon landing on tallon.
• Furthermore, Metroid Prime counts % as what Samus has (as opposed to what she collects), so if item loss skip were still possible, she would start with several % already upon landing on Tallon Overworld.
• Varia Suit can be skipped, which makes 20% the actual lowest%, but it requires a TAS only secret world in Transport to Tallon Overworld South.
• All 12 artifacts are required to access impact crater.
• Phazon Suit is required to damage Metroid Prime phase 2, but it doesn't count towards % at all.

21%

Collected

• 12 Artifacts
• Missile Launcher
• Morph Ball
• Bombs
• Varia Suit (traverse Magmoor without e-tanks)
• Wave Beam
• Ice Beam
• Plasma Beam
• Main Power Bombs (Phazon Elite container can't be broken without main power bombs, to get artifact of warrior)
• X-Ray Visor (can't damage Omega Pirate without this, meaning no Phazon Suit)
• Phazon Suit (required to damage Essence; doesn't count towards % counter)

Skipped

• Charge Beam
• Boost Ball
• Space Jump
• Super Missiles
• Thermal Visor
• Spider Ball
• Gravity Suit
• Grapple Beam

Metroid Prime 2: Echoes

Notes

• With Item Loss Skip, you start with Missiles, Bombs, Space Jump, Boost Ball, and Spider Ball.
• Item Loss removes all of the items currently in your inventory and sets your percentage to 0; all items obtained prior to Item Loss don't count towards %. Without using Item Loss to reset the percentage counter, 6% is currently the lowest possible percentage. 5% (-Dark, -Light, +Annihilator) has been hypothesized but isn't currently possible because it isn't known how to transition into upper hive.
• Although Item Loss does remove all 3 beams and their ammo from your inventory, it doesn't take away the ability to use your currently equipped beam (you do lose this ability if you ever switch to Power Beam). Any one of the three beams can be "kept" using this method, but for 4% you must "keep" either Dark Beam or Annihilator Beam in order to open dark portals. Regardless of what beam you keep, you can't keep any ammo and are forced to use charged normal shots. 4% Light keeps Annihilator while 4% SJ keeps Dark.
• All temple keys do not count towards %.
• All 9 sky temple keys are absolutely required to unlock the Sky Temple and are taken away from you after item loss.
• Dark Visor is absolutely required to pop the key storage pods, and Light Suit is required to collect some of the keys. Because of this, both 4% routes require you to pop all of the key pods prior to Item Loss, but the route that collects Light Suit prior to Item Loss must collect all of the keys and unlock the Sky Temple before doing Item Loss, while the route that collects Light Suit post Item Loss must pop the pods but refrain from collecting any of the keys until after Item Loss.
• It is not currently possible to kill Dark Samus on hard mode under 4% conditions; 5% is currently the lowest possible percentage on hard.

4%

Collected (post Item Loss)

• Morph Ball Bombs (Emperor Ing 2)
• Spider Ball (Emperor Ing 2)
• Screw Attack (needed to pretty much do anything)
• and one of the following to kill Emperor Ing 3:
• Space Jump
• Light Suit

"Skipped"

• Missiles
• Violet Translator
• Amber Translator
• Light Beam
• "Dark Beam"
• Dark Suit
• Super Missiles
• Emerald Translator
• Boost Ball
• Seeker Missiles
• Gravity Boost
• Grapple Beam
• Dark Visor
• Cobalt Translator
• Main Power Bombs
• Echo Visor
• "Annihilator Beam"
• and one of the following:
• Light Suit
• Space Jump

6%

Collected

• Dark Beam (needed for doors and portals)
• Light Beam (needed for doors and portals. is skippable but skipping this requires many other upgrades)
• Dark Visor (needed to get any sky temple key)
• Main Power Bombs (sky temple key in dark oasis never appears until this is collected)
• Screw Attack (needed for many out of bounds to skip other upgrades)
• Light Suit (can't enter ingswarm nor poison water for many sky temple keys)

Skipped

• "Missiles"
• Violet Translator
• "Bombs"
• Amber Translator
• "Space Jump"
• Dark Suit
• Super Missiles
• Emerald Translator
• "Boost Ball"
• Seeker Missiles
• Gravity Boost
• Grapple Beam
• Cobalt Translator
• "Spider Ball"
• Echo Visor
• Annihilator Beam

Metroid Prime 3: Corruption

15%

Collected

• 1 energy tank (the one in GFS olympus at the start)
• 1 energy cell (the one for seeker missiles)
• 1 ship missile tank (the main ship missile upgrade is skipped; getting an expansion lets you use it though)
• Missile Launcher
• Grapple Lasso
• PED Suit
• Boost Ball
• Plasma Beam (Required for several doors)
• Screw Attack (Required for skipping the skipped items; is skippable otherwise though)
• Seeker Missiles (Required for Helios Seed)
• Hyper Missiles (Required to unlock Pirate Homeworld)
• X-Ray Visor (Required for terminals)
• Grapple Voltage (Required for code on Valhalla)
• Nova Beam (Required to damage Omega Ridley and for getting out of Valhalla)
• Hyper Grapple (Required for the code in pirate homeworld)

Skipped

• Grapple Swing
• Ice Missiles
• Main Ship Missiles
• Hyper Ball
• Ship Grapple
• Spider Ball
• Hazard Shield