That’s true. They’ve almost all seen tremendous scope creep in terms of their powers. Not just Logan.
As for Romulus, I just ignore most of that stuff. I did kind of like the thought that a shadowy figure was manipulating the events of Logan’s life, keeping tabs on his family due to their genetic potential and then kind of orchestrating events along the way to some extent… but that sounds a lot like something Sinister would do versus Romulus… and we do know Sinister worked for Apocalypse for many, many decades prior to them splitting. En Sabah Nur is who imbued him with his powers and longevity, after all. So that fits much better IMO.
Sinister keeping tabs on the Howletts and specifically Wolverine over the years, and ultimately Apocalypse being behind Weapon X fits sooo much better than Romulus. After all, if the Apoccy’s mission was “survival of the fittest” and creating the strongest mutants possible… wouldn’t taking a mutant already born with incredible genetic gifts and enhancing him to make him stronger — so that he’s basically a super assassin capable of killing super soldiers in an age of superhumans — fit with that mission? Seems to me it would. Plus Logan’s line would be known to Apocalypse via his encounter with his ancestor, Folkbern Logan, in the Middle Ages. See Uncanny Avengers for that one.