Well, i do not actually like "level scaling", but...but this game actually need some form of level scaling to keep player from reaching "endgame" under single hour of game play.
Also i do not like seeded based loot, there are no reasons to use seeds instead of actually preplacing all loot directly, to support "looting skills", additional sections may be generated and stored, additional sections can be used by mods, or for story content.
As for story and progress, instead of just trying to explain, i will provide link to "live" implementation of system:
http://wogen.wikia.com/wiki/Gothic_3_Unique_ChestsTLDR, "chests" have 3 sections, first section is level scaled loot, that depend solely on level of player, at moment of chest opening, second section, is random scaled loot that depend on chest location (area level), third section is "list" of weapons that appear in specific order, ignoring player level and position of chest in the world.
This system can be used in SS to prevent player from getting paragon from first research station, perfect world inside very first yellow star system ever entered, and at same time, may be used to ensure, that perfect system and paragon will eventually spawn, no matter how unlucky player is.
As for planets, as long as player not actually entered system (or performed full survey), world feature may stay unfinalized, world is "habitable" but it's type and planetary features are not picked from list.
This can be used to delay "good" planets by picking "bad" modifiers from list, and later, reverse effect, by picking "good" modifiers from list, it may ever be used to spawn "gaia" world in exactly very last yellow star system explored by player.
This kinda kills "rogue like" spirit, but, it will provide smooth and rewarding gameplay, instead of spiky and jiggly "curve" of happiness and frustration (mostly frustration).