Nor is the lack of their presence something you can assume is evidence for their retirement.
Sure it is. It's an indication of scarcity. It's only one piece of evidence, but that's one more than you've got.
You assume they even see it as a design flaw that they destroy subspace nodes when it blows up, perhaps it's not, perhaps it's a defence mechanism if an enemy is technologically advanced enough to do it then they consider the specie enough of a threat to seal them off entirely, on an intergalactic scale one system is insignificant (even to the ancients, let alone the shivans).
I've not commented on this point much, but the basic theory is that if the Shivans care enough to dispatch a
Lucifer to kill you, leaving you unreachable to develop further now that you have a reason to attack Shivans is not wise. I can't concieve (and I doubt anyone can) of a situation where armed conflict will not matter to later situations. Don't leave an active enemy behind you is a principle any form of life that will engage in warfare would appreciate.
I haven't been making assumptions, I have been offering counterpoints.
Then what were all those things without evidence you offered? Your
speculation on Shivan strategic aims, numbers, reach, resources? We don't
know any of those things, they are assumption.
If anywhere they visited was suspect (and, you're failing to understand again) then the ancients would have been likely to discover the technology from a specie that existed before them as well.
Why?
The Ancients realise that the Shivans had been in the area before the Ancients ascended to power already.
Cite your source. (Bosch Monologue does not offer conclusive proof; even he phrases it as speculation!)
You assume the Shivans even give a crap about psychological warefare when the only evidence pointing to them doing so (ever) is the Lucifer heading as directlyish as possible to both Vasuda and Sol.
This is wrong on both counts.
You were the one who assumed the Shivans gave a crap about pyschological warfare. Your exact words are "The Lucifer as an untouchable Super-Destroyer in normal space has a much greater psychological impact on a specie", and you can find them in my last post. I make no such assumption; I merely note that Shivans seem to understand and exploit manuver warfare concepts in FS1. Task overload is a pyschological concept but it's fundemental enough you can do it to computers: simply present it with too many things that need responding to at once. Unless you're claiming that's impossible to do to a Shivan (unlikely at best), they'll understand it.
The Lucifer also did not make a direct journey to Vasuda, futzing around a good bit first; Ribos is not on the direct route to Vasuda from Ross 128 but the
Lucifer turns up to destroy Tombaugh station anyways. It similarly did not make a direct journey to Sol, otherwise you would never have had the time to win the game; it notably appears off the direct route in Altair during Running The Gauntlet.
Even the fact that the Shivans might be of separate factions is still possible/as likely as yours.
I've never pretended otherwise. In fact I rather like that theory.
It's not, however, the theory you're supporting.
As for the Shivans being around for a long time, it's mentioned in the Ancients dialogue, you don't even know the games so why are you even bothering to write theories on the lore?
I know the dialogue better than you, apparently (see above), and no, it's not. It's just mentioned in the Ancients dialogue that they were around at the same time. You are perhaps thinking of one of the Bosch monologues but that's phrased by him as speculation.
My point is not to proffer a competing theory, it has been to point out that you could so easily be completely-wrong.
You don't know, at all, so why?
Bad logic is bad logic, and I will attack it wherever it appears. So far all the arguments offered that I'm wrong have been bad logic. Also the retirement theory has more evidence, admittedly circumstantial, but still more, than the one the Lucifer has been maintained in service.
Perhaps Shivans don't build ships, but grow them, perhaps Shivans don't grow ships they ctrl-left click, Perhaps the Shivans are dealing with a finite series of ships and haven't constructed any for the past few billion years and therefore can't afford to retire Lucifers.
Speculation, and therefore useless to the discussion.
Perhaps the Shivans in their grand majesty DNA altered Apes to evolve into Humans and beyond 
Now you're just bull****ting. You actually trying to argue something logically here or what?
Perhaps the game designers decided that it would make the original unplayable if the TERRIBLE AND UNDYING UBERSHIP OF DOOM became a common destroyer.
We're discussing things in-universe, reaching outside is verboten. Sorry.
You assume they even have a tactical/strategic plan of action to combat alien specie, I mean, YOU might be really OCD but would you have a tactical/strategic plan of action to combat an ant infestation? Or would you just pour hotwater down the holes they come out of?
If it were really a matter of combating an ant infestation, there would be no cruisers or fighters or destroyers deployed against us. You know that. This may be a campaign of extermination, but it's still a campaign. There's no hot water here. There are warships, and they are making war. The games are a two-way street; we kill Shivan fighters and cruisers and destroyers, usually in similar number to those of us they kill. They may be bits of a numberless horde that's somewhere offscreen or they may not, but the mere fact they're taking losses makes it a war.
Also to the point, lots of people make good money studying the best means of application and the best pesticides to use in reality.
There's /plenty/ of emotional/human military crap in your comments the entire things you post are based on those concepts as such.
You're not producing the evidence still.
I have no reason to believe you.