Better early game

"Derelict/abandoned/dead ships or stations within systems that can be reactivated by the player or the AI allowing for bonuses, new ships, new research, event chains etc. Stellaris does this fairly well, and it adds a lot of flavour to the early game."

This is effectively already implemented in the game.  Some signal anomalies and some quests triggered by anomalies result in the player salvaging derelicts that join their fleet.   Some even spawn pirates!   Rut roh!  

"Flavoured diplomacy based around the faction's core ideals - I appreciate that this is in the game, but at present in the early game you are more likely to be the targhet of animus than a more pragmatic approach to trading - If the Sophons are light years ahead with tech surely a better trade system would allow for a golden hello"

I've, to my mind, found the diplomacy to be quite flavorful.  The Vodyani won't ally unless you're not a target of their crusade, the  Unfallen prefer to ally, the Riftborn are no pushovers, but if you treat them right, they'll gladly at least declare peace.   Have you tried proactively engaging in diplomacy?   You usually have to bribe factions of relative/stronger strength into peace, from there it's much easier to negotiate trade.

"Allow a more rapid expansion without tanking moral for the player, as this will enable players to get a decent foothold before the AI comes banging on the door. This could be encouraged through the foundation of science/trading/spy/fortified colonies that as long as they focus on the core attributes of the faction for a period of time will not reduce down the moral of the established systems"

My solution to this, and it's worked up to Impossible difficulties, is to use a colossal galaxy.  It may be turn 50 before you even encounter another major faction.   Some of the 'flavor' and 'excitement' present in 4X *is* having no time before the AI comes banging on the door.  If you choose a smaller galaxy, you can expect them to be meeting you quite soon.   I do like the idea of a way to fortify colonies, but that kind of defeats the purpose.   When an AI colonizes within my borders, I like to be able to blockade it to death quickly so I can free my fleet up for the inevitable fallout.

"A series of random, though flavoursome, events that really amplify the nature of each faction. I.e. if you'r playing Sophons double down on the go big or go home research ethos."

Your faction quest triggers quite early, but I do admiit that sometimes there's less randomized events in the beginning.  I'm usually too busy rushing to boost FIDSI and expand to all the tastiest systems to be bothered much with quests in the early game.  I guess we have different apprroaches.   Endless Legend takes longer to expand in, there's more of a personal feel to each settlement you have, ES2 (especially on larger maps) demands a certain speed to growth, or you'll get left behind.   That's why I haven't mastered the Unfallen yet.