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I think this was actually a series of books following the human survivors of an alien invasion of Earth. Set a little into the future though I don't think it's by much. Strangely the aliens have ships which are nuclear-based and not much more advanced technology-wise than second world war. I think Morgana is featured in there as the person who advanced the aliens' intelligence to the point they became space bound and then encouraged them to invade?

Merlin is also featured as a dotty but powerful old man with Excalibur being an excessively advanced high tech spaceship which "Arthur" is the only one who can mentally connect to in order to fly it?

I can't find much about it online, but the Dyason series by Warren James Palmer has similar elements.

Summary of the first book, Empire of the minds (1995), from Amazon:

By the year 2045 the United Nations World Defence Force can finally guarantee the security of every nation on the planet through the use of orbital laser battle stations.
That is until the day the Dyason arrived. The Dyason are humanoid, but not from our star system. In a blitzkrieg attack they wipe out the World Defence Force and within days, force worldwide capitulation. except for a few renegades, mankind is enslaved.

Out of the prison ghettos of London a new hero emerges, a youth with exceptional mental powers. Minds of the Empire follows Moss as he struggles to escape the rubble of London and flee from both the Dyason and the Resistance.

Checks:

• not too far future (2045), survivors from alien invasion of Earth


• it's a series


• a review here explicitly mentions "King Arthur legends".


• 
  the summary of the second book, Dominator (1996), has the aliens coming back with bigger, badder ships, and Earth relying on Excalibur, a spaceship which was found under Stonehenge, to protect it. Excalibur is then presumably quite high-tech.


• Moss, the protagonist, has "mental powers". He might, or might not, be able to "mentally connect to the ship".

Not sure if checks:

• I can't find anything about Morgan, but there is little to be found online on that series, so maybe it was a later twist that nobody wanted to spoil?


• Merlin is featured, but then again, Merlin is never far from Excalibur, so that's not much of an indication.

Found with the Google query book excalibur spaceship which returned this self-answered Reddit thread:

Scifi series from 20ish years ago, young adult, kids book, alien occupation, London, Merlin, Stonehenge, spaceship excalibur, telepathy/telekenesis

Series of pulpy young adult scifi books follows a british boy, initially living in London on an alien occupied earth. Boy character leaves London after botched assasination attempt on an alien possibly at a theater, finds spaceship excalibur and merlin under stonehenge?, unlocks latent telepathy/telekenesis and over 2 or 3 more books takes the fight to the alien planet. Bought in 1995 +/-10 as paperbacks from a budget bookshop on Charing Cross Road. Possibly published or printed by independant 'ripping yarns'.

Almost surely not the answer (no Morgana, which features prominently in your question, no "backward" alien ships), but otherwise a close fit should anyone come here with this in mind:

• starship called Excalibur, manned by Earthmen (well, sort of)


• Earth invaded / menaced by galactic aliens


• an invasion (actually extermination) fleet

...all appear in David Weber's The Excalibur Alternative, chronologically in year 2097 if memory serves, more or less last installment of the "Earth Legions" (formerly Ranks of Bronze) series.

The funny thing is that this other piece of question

Strangely the aliens have ships which are nuclear based and not much more advanced technology wise than second world war

appears in The Road not Taken, which has a plot point in common (aliens "invading" and more or less unwittingly supplying space flight to Earthmen) with Anderson's The High Crusade, itself similar to Earth Legions.