Originally the ending was supposed to have Tear hug Luke but that was scrapped on the last minute. Others can say this points to Asch, while I have to question what kind of writer would even think of a Tear hugging scenario when it's supposed to be Asch. I can't imagine an author going, "Ok Asch returns, right? So let's imply that by having Tear hug Mr. Ending and make it a happy reunion scene..."
Asch's left-handedness while logical and natural ('cause he's the original) isn't as significant story-wise when compared to the fact that he's right-handed. There's a reason why he's right-handed and why Luke is left-handed. They're like a mirror images of each other. And also when the camera shows the position of the hilt and the way the Key is worn across the back, the scene is emphasizing something revealing. Story-wise, not once in the game was Asch even revealed to be left-handed. It was only in an interview after the Perfect Guide was released that this was mentioned. Moreover if left-handedness was to determine Asch more, I would assume he would carry his sword on his left hip and not imitate replica Luke all the way...which isn't the way I imagine Asch would go.
Similarly we have that revelation about how Tear was supposed to hug Luke in the end. I count this right up there with Asch's left-handedness in the sense that it's a piece of info revealed in some interview during its peak after-game hype. And while the contamination events end with Dist getting pissed off at Jade for siding with Luke, and thus going against his very own research, one can't simply ignore what happened to Star. Then, there's also the theme song "Karma" which basically hints that it's Luke that returns, which in this case makes both Jade and Dist wrong. What you think Jade's facial expression meant in the end basically reflects the opinion of the player.
Looking at the board, I'm shocked re: the debate on whether or not Luke survived in the end, and met Tear and co. at the Valley. I thought that was apparent, given the symbolism that permeated the entire story, and the overall arc for Luke. But since there is a debate, I thought it would be a good idea to focus on the story from a literary perspective (since it was written ostensibly by a group relatively well-versed in literature, no?) and point out why there is little doubt that Luke returned.
Many are focusing on the appearance of Luke as proof of a 'new' Luke - a fusion between Asch and Luke following Lorelei being free. And I think that's a valid point. But I think the imagery suggested is a metaphorical growth on the part of Luke, not an actual physical 'fusion' of Luke and Asch. When Asch died, Luke mentioned that he 'felt' Asch, and that Asch was with him in the final sequence. Luke was furthermore able to use the second degree hyperresonance during the fight with Sync - something that is implied by Jade to be outside the realm of the abilities of a replica. So 'Luke" was well on the way to becoming a new, complete being before the ending proper. As Asch faded away, Luke grew closer and closer to a 'complete' being (metaphorical sense, but literal).
It's also important to look at what Asch represented - Luke's past, his self-loathing...etc. From a literary standpoint Asch is Luke's foil: the 'obstacle' that Luke has to overcome to be a complete being. That's why it was crucial for Luke to fight Asch at Hod: he had to overcome his own insecurities and fears. Luke only grows (relatively speaking) as a character when Asch is present. First when he doubts the core of his existence: Asch is a large part of the motivation for his change. Then when he accepts the burdern of his power: his major sacrifice comes as a result of his trying to make a choice; that's why Tear's decision to allow Luke to decide on his own is important, and Luke's fear of dying even more so. Finally, the last 'growth' for Luke comes in the fight with Asch - this is where Luke's resolve to defeat Van is really born. It's the attitude that is shown in the conversation during the final fight, and the reason why Luke *outright says how he's found value...etc. defining his life*. You can get even more detailed at this point and talk about Guy's comments re: life and the thematic significance of the dialgue between Tear and Luke right before the final anime cut-scence.... but I'm draggin this out. Last point: the BGM title for the music during the fight is "meaning of birth" in the English V. If the title is similar in the JAP version, then this pretty much solidifies the thematic importance of Asch: as an aspect of Luke's persona, crucial to the birth of the new luke. Luke's conflict with being a replica, Asch's comments about Luke 'replacing' him, all of it falls under this theme of self-discovery.
To end finish up the talk re: apperance, it's important to adress the hair. Asch has long hair - that is part of Luke's past. Hair is actually a pretty crucial symbol re: character growth. But Luke's present involves his snazzy short haircut. In the cut-scence, his bangs ( think that's the word - the front of his hair) is the same as it was - roughly - when it was short. Thus, 'new' Luke is born - the mature version of the old Luke, who has accepted himself and his failures, burdens...etc. Most importantly: Luke promised Tear he would change. And he did, and his convenant was made by cutting his hair. It's very Elizabethan to have the hair grow again at the end, to show that Luke is both the same and different.
It's important though to understand that while Luke is in appearance 'new' this is superficial and symbolic, not representative of a physical change.
Next, and this is very important re: the ending: the setting and the *conversation* about the setting. Guy and the others talk about the coming of age ceremony for "Luke fon Fabre" at the mansion. But they aren't there, as they're not fully part of that aspect of Luke's life, of his past. It's important to see what the Fabre manor is associated with in this game: first with a lack of freedom (opening sequence, obviously), then with a lack of peace (following Van's first defeat). Luke returned to the manor once, but that was not 'home' to him - which is why the events re: the letters and his trip to see Tear are crucial to the plot. This rejection coupled with self-discovery is apparent when he brings in Asch to see Duke Fabre - Luke rejects the manor as his own consciously and tries to supplant that relationship with Asch, and Asch (again representing an aspect of Luke's psyche) rejects the manor as part of who he is.
So it's important for Luke not to be at the manor in the ending sequence, because he is in essence rejecting the "Luke fon Fabre" and Asch personas. Both are part of who he is (hence the new apperance) but neither define what he is. Which is why the Tartaroo Valley is so important: because it is 'home' for Luke. It's where he met Tear, where he began his growth. He came back at night, too - and that's significant, because he was there with Tear at Night. I wouldn't be surprised if both glanced at the moon at that point (haven't replayed yet) but it would be very symmetrical with the type of ending cut-scene. The Selenia flowers were present during Luke's transformation, too: (1) when he left the manor, and began his journey; (2) when he cut his hair, and began to reject "Luke fon Fabre"; and (3) when he left his 'home' to meet Tear following Van's first defeat, he met Tear in Yulia city amidst the Selenia. Pretty important parallels - every seperation/meeting between Tear and Luke is unified with the flowers.
This leads to the comment of "please, come home." Since Luke became something new, and reject his old persona, the Fabre mansion is not his home. Asch is dead - that's the part of him that he left behind at Hod. So his 'home' is more of an ethereal place, where his heart belongs. This is why the conversation re: the manor is crucial prior to his appearance, as is Tear's question of "Why are you here?" Because it draws attention to the fact that he's not at the manor. When Luke responds with the "I made a promise," line, he's pretty much implying that he came home, and that the manor was not his home.
So the new apperance, the setting...etc. all essentially exist to show that Luke has grown, that he's become a whole being. Tear crying just solidifies the point.