Off the top of my head, make the Black Fleet (Pyramid ships) into a mid/end game crisis. Alternatively, look into the Shroud stuff and maybe make it so you can make pacts with the Darkness/ get boons from the Light.
Pre generated empires for Hive, Cabal, Eliksni and Vex.
Archaeology Sites leading to relics like Ahamkara Bones, maybe a Shard of the Traveler/ Crux of Darkness.
Pyramid Ship Set?
Arc Solar and Void Light deposits for various buff or perhaps special equipment?
Ascension Perks unlocked by meeting the Traveler or a Pyramid

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Off the top of my head, make the Black Fleet (Pyramid ships) into a mid/end game crisis. Alternatively, look into the Shroud stuff and maybe make it so you can make pacts with the Darkness/ get boons from the Light.
Pre generated empires for Hive, Cabal, Eliksni and Vex.
Archaeology Sites leading to relics like Ahamkara Bones, maybe a Shard of the Traveler/ Crux of Darkness.
Pyramid Ship Set?
Arc Solar and Void Light deposits for various buff or perhaps special equipment?
Ascension Perks unlocked by meeting the Traveler or a Pyramid

I very much agree with most of this, but perhaps have the Taken or Vex act as mid-game crises.

Even better, have it be a chance between Hive and Vex. Either the moons of Fundament align and the Godwave inspires the creation of the Hive, or have the Black Garden open and the endless swarms of Vex pour through as a Midgame, while the arrival of the Black Fleet in the endgame signals the start of a galactic Collapse

In addition, different ascendency paths for Light and Darkness, leading up to Lighbearer and the ability to Take somehow. Should probably be spiritualist based a bit.

Hope its not too much trouble but a suggestion is the ability for the Hivemind to grow into Hive magic, perhaps creating their own subspecies that is almost like the Hive but is separate from the Hive if that makes any sense. The same idea for the Machine Empires having the chance to be able to grow into Vex tech.

House of dusk,More anaomtlies, more events, techs (fallen,cabal,hive,taken,vex and more), home systems and systems,

I'd like to see the Traveler as an origin as well, unlocking it from the start for those really interested in it.

I hope it's not too much trouble suggesting to add some Rasputin stuff, it would be so cool to control a hive mind with its characteristics and maybe "warsats mechanics"

In addition to the elemental deposits mentioned, maybe also add in a Stasis deposit? Maybe once you meet a pyramid ship you unlock the technology to harvest stasis or something

If you can keep the traveler and make Guardian armies and have a chance for dead leaders to become a Guardian.

Maybe a Vex gate event where on of our worlds we come across a vex gate and we have the option to explore it leading to the Black Garden?

Are there any Galactic Community and/or FE/AE interactions with The Traveler? Or are these things that are planned for future?

Warmind building. Maybe like a unique one build and several smaller stations for like naval capacity and such