Continuity mistake: When Chewbacca is choking Lando, as Leia says, "We don't need any of your help.", Lando is standing on his knees. In the next shot, only his head can be seen, but the position of his head and Chewie's arms shows that he is now standing straight up. In the next shot, he is on his knees again. (01:38:15)
Continuity mistake: After Boba Fett's ship, Slave 1, takes off, there's a close-up of Leia's face. In the background, Lando can be seen standing erect, putting his hands on his waist. In the next shot, he's crouching, with his hands in front of him. (01:39:25)
Continuity mistake: When Luke and Vader are fighting in the carbon-freezing-chamber, Vader says, " You have learned much, young one." Their light sabres are held in different angles between this shot and the previous and following shot. (01:39:40)
Continuity mistake: When Luke summons his lightsaber back to his hand during the duel, he's holding onto a hose with his other hand. He is holding it differently from the previous shot. (01:40:25)
Continuity mistake: Widescreen version: When Luke and Vader are fighting in the carbon-freezing chamber, as Vader says, "Only your hatred can destroy me.", the hose hanging from the ceiling behind Luke is pointed straight down, but in the previous shot, it was bent. This has nothing to do with camera angles - watch the smoke coming from it, it changes direction as well. (01:40:40)
Continuity mistake: During the first scene in the lightsaber duel, Luke is holding his in different angles between shots, depending on the camera angle. (01:41:05)
Continuity mistake: When Luke is sucked out the window, there are no wounds in his face, nor when he hoists himself up on the platform. But when he runs into Vader again, there are. (01:42:35 - 01:45:10)
Continuity mistake: After R2-D2 opens the door to the landing platform during the escape from Cloud City, the droid exits through the door. Some shots later, he is back inside. (01:43:55)
Continuity mistake: After Boba Fett's ship takes off, C-3PO yells, "Oh no. Chewie, they're behind you." Chewbacca shoots at the newly arrived stormtroopers and one of them falls over dead, next to the big white sculpture at the top of the stairs. In the next shot, where R2-D2 spins around before going after the others, the stormtrooper's body is gone. (01:43:55)
Continuity mistake: When Vader and Luke are fighting in the carbonite freezing room, before Luke falls into the chamber, you can see the doors of the freezing chamber closed. In the next shot you hear the doors begin to open, but you can see that the doors are already completely open. (01:44:05)
Continuity mistake: When Leia and Lando are holding off the stormtroopers while Chewbacca and the droids escape into the Millennium Falcon, a stormtrooper comes running through the doorway. You can see the burn mark on his armour before Lando shoots him. When the trooper is shot, another trooper comes running through the door, also with a burn mark on his armour. Then Leia shoots another (or perhaps the same) trooper, and the burn mark is once again there before the trooper is hit. (01:44:20)
Continuity mistake: During Luke's and Vader's lightsaber duel, Vader says, "Release your anger" and in the next shot their interlocked lightsabers have switched positions. (01:44:50)
Continuity mistake: When Vader cuts through three poles at the end of the lightsaber duel, there are different poles in the shot where he cuts through them and the next shot where they fall. The poles that are cut have a white color, while the ones that fall are dark grey. (01:45:50)
Continuity mistake: When Vader cuts through the three poles at the end of the lightsaber duel, Luke is crouching down next to them. In the next shot, he is standing upright. (01:45:50)
Continuity mistake: In the shot before Luke's hand is cut off, his left arm is bent and his elbow is positioned next to a pole. In the next shot, his arm is straight and his elbow is next to a different pole. Also, his lightsaber is held in a different angle. This is best seen in the widescreen version. (01:45:55)
Continuity mistake: When Vader cuts off Luke's hand, as the shot ends, Luke is standing upright, but in the beginning of the next shot, he has already began to drop down. (01:45:55)
Continuity mistake: During the duel in Cloud City, Darth Vader cuts three pillars with his light saber, just before cutting Luke's hand. The pillars aren't burning after that yet in the following shot, they are burned. (01:45:55)
Continuity mistake: Widescreen version: In the shot where Luke's hand is cut off, two of the poles that Vader just cut through can be seen in the lower right hand corner. The poles are much closer together than in the rest of the scene. (01:45:55)
Continuity mistake: When Luke drops down in pain after his hand is cut off, he is not holding onto the pole with his other hand (watch closely), but in the next shot, his hand is now clutching the pole. (01:46:00)
Continuity mistake: When Vader attempts to turn Luke to the dark side, he says, "With our combined strength, we can end this destructive conflict and bring order to the galaxy." As the second shot begins, Luke is standing much closer to the structure he's holding onto, than in the previous shot. (01:46:20)
Answer: The short, short answer to this is "Yes... from a certain point of view." The long answer is complicated and depends completely on what timeframe you mean by "always." If you're going back all the way to the early rough drafts of the early-mid 70s (which actually resemble Episode I more than they do the Star Wars of 1977), you'll find there's a cyborg father figure protagonist that makes a heroic sacrifice, and then another character that is a "black knight" villain that eventually turns to the side of good near the end. Just to make things more complicated, there is yet another character, a villain by the name of "Darth Vader" that is a human Imperial officer like Grand Moff Tarkin. It may be a stretch to count all that as "Darth Vader was always the father" but the pieces were all there, at least.
TonyPH
(1) Now the earliest explicit mention on any documented material that Darth Vader is Luke's father comes from notes Lucas made outlining the general story of the trilogy and its place in the larger Star Wars saga. These were found in the archives for The Empire Strikes Back, but they are undated and we don't know if they were written before Star Wars (1977) and carried forward, or if they were written afterward. These were found fairly recently (made public in 2010) and as far as I know Lucas has never commented publicly about them.
TonyPH
(3) One thing we know, at least, is that Lucas had come up with the idea of Darth Vader the father before starting work on The Empire Strikes Back. Something incredibly odd, though, is that the first draft written by Leigh Brackett does not feature the twist (and in fact introduces Anakin himself as a ghost); for a long time many fans took this as proof that Lucas hadn't thought of the idea at all by then, but after the series outline was discovered it was made apparent that Lucas simply hadn't told Brackett for some reason. Perhaps he wasn't sure yet that he wanted to go through with it, or maybe at that point he was thinking of revealing it in the third film. Either way, Lucas would write the second draft himself, and that's where the twist first appears in script form.
TonyPH
(2) Something that must be understood about Star Wars (1977) is that it was an ALTERNATIVE to his original plans of a saga. By then he didn't think it was realistic that he would be able to make a long series of many movies, so he came up with a "Plan B": he crammed the general story of the trilogy into one movie. So we know that when Star Wars (1977) was filming, Darth Vader was NOT Luke's father, because this one movie was IT, that was the whole story. But what we DON'T know, is whether that means Lucas had abandoned the idea of Vader being the father in order to simplify the story, or if Lucas simply hadn't thought of that at all just yet.
TonyPH
(2, cont.) On a side note, you can tell by watching Star Wars (1977) how it has condensed the story of the trilogy. The middle portion has the characters trying to escape capture from the Empire while one of them loses a duel with Darth Vader (like The Empire Strikes Back) and the third act is a final battle against the Death Star above a forest moon (like Return of the Jedi). The first act features a member of royalty on the run while a couple of protagonists find the main hero on a desert planet, resembling the original drafts and by extension Star Wars: Episode I. Because of this we've arguably never actually had a "pure" first chapter to the original trilogy, even though Lucas eventually had the film serve this purpose anyway.
TonyPH