Counting 3 as DS and DS director's cut have separate trophies, and actually play out a little different as the DC release adds more tools early on so it feels a lot less "survival"-ish.
None of what you describe is actually a ret-con, because the whole actual backstory with Lucy is not something that Sam would have been aware of. To be honest it all fits to me way better than Cliff's sub-plot in the first game, and as a whole I found the story in the sequel to be way, way better because its less burdened by long scenes of dry exposition.
Also the emotional manipulation of the third act at least feels earned in the sequel's storyline, whereas the whole "take Lou to the incinerator" bit in the original always fell completely flat to me as it essentially came out of nowhere and were it not for the predictable last-gasp twist would have been such a cheap and pointless bummer ending that it never occurred to me as a potentially realistic outcome.
DS2 is just a way, way better version of the core concept in my view. I also really appreciated the lighter overall tone and the way that Kojima fully embraces the sandbox aspect from the start, rather than back-loading it so heavily like the first game.