This is the current development "road map" that I have in mind:
Version 2.1: Initial release - This is what we're currently working towards.
~Consists of the majority of the base mod elements
~Bosses currently included: Torizo, Serris, Kraid, Phantoon, Nightmare, Omega Pirate
Version 2.2: Prime Update - Consists of additional Metroid Prime content
~Will include an Impact Crater-esque dungeon that houses the Metroid Prime, a Moon Lord tier boss that grants the Phazon Beam.
~Plus other additional things.
~Bosses currently included: Meta Ridley, Metroid Prime
Version 2.3: Echoes Update - Metroid Prime 2 content update
~Will introduce an alternate dimension that will be a dark variant of the player's current world (will be named "Dark [WorldName]" in the mod, also known as "Dark Aether" in Prime 2).
~This update may be primarily focused on the Dark World and as such most of the content may revolve around it.
~How the Dark World will be implemented is still being decided.
~Bosses currently included: Amorbis, Chykka (Larva/Adult), Quadraxis, Emperor Ing, Dark Samus (or "Dark [PlayerName]")
Version 2.4: Corruption Update - Metroid Prime 3 content update
~Introduces P.E.D. (Phazon Enhancement Device) Suit that has the Hyper Mode functionality, and all of the pros and cons that come with it.
~May include Leviathan Seeds, special Phazon dungeons that house special bosses. How they will be implemented is still being decided.
~Bosses currently included: Mogenar, Helios, Omega Ridley, Dark Samus (Prime 3 variant), Aurora Unit 313
Version 2.5: Yet Another Metroid 2 Remake Return of the Terrarian Update - Metroid II: Return of Samus/Samus Returns/AM2R content update
~Greatly expands on Metroids by adding their different evolutionary states.
~Will add "Metroid Nests" that consists of layers - (tentative) first layer will have Gammas and Zetas, second layer will has Zetas and Omegas, third layer will have Omegas only, and in the center is where the Queen will be.
Version 2.6: Super Update - Super Metroid content update
~Will add Tourian, a hidden Space Pirate base connected to vanilla Terraria's dungeon. Inside lies the Mother Brain, a Moon Lord tier boss that grants the Hyper Beam after being defeated.
~Bosses currently included: Ridley (if he isn't introduced earlier), Draygon, Spore Spawn (maybe), Botwoon (maybe), Mother Brain
Version 2.7: Fusion Update - Metroid Fusion content update
~We'll cross this road when we get here.
Keep in mind that this lists tentative and WIP stuff, so it may not represent final decisions. And I also left out minor updates that could add things such as Space Pirate invasions, and other tweaks or small content additions. (These updates would be listed as "2.1.x" or what-have-you.)