There are visual cues and there are other visual cues. Not trying to make a super villain out of him because he's not. I don't know about other fans and their attitude but I'm just speaking about things within narrative. And the entire premise of becoming stronger (for "paceful purposes", protection, making your dreams a reality) seems like a very important theme, not to be ignored. So in Alan's case, one (keeping Manon/Platane safe) and the other (being stronger) interconnect with one another.
Otherwise he wouldn’t even do stuff with Lys in the first place. So while he did play this whole thing harshly - yes, clearly on purpose - the seed of some truth was there. He can’t become stronger WITH manon (the way he “needs” to be) because he can’t expose her to danger. And he’s only in potential danger because he pursues energy for Lys, which he does willingly and passionately. I feel they’re trying to play a self-sacrifice motive here, one which may (somehow) mirror with Lys (“pure” boy).
“There are visual cues and there are other visual cues.”
That sentence … doesn’t actually mean anything. I’m not trying to be rude here, but when I bring up the visual cues I’m talking about the specific ones that I pointed out in my initial reply to you, using screencaps not only from the scene in question, but showing how they mirror to other scenes within the series as a whole to show that the PokéAni team was employing a technique that they have specifically utilized in the past to show when a character is being dishonest with their feelings (and one that is very easy to pick up on even if you’re not familiar with the techniques of the studio). When it comes to a visual medium such as animation, a character’s eyes are incredibly important. “The eyes are the windows to the soul” is a cliché to be sure, but it is an effective one. That the PokéAni team capitalizes on this in order to show a character’s emotional dishonesty or discontent by shadowing their eyes so that they can no longer be seen—and that they have always done this, even as far back as the Original Series—means something. That we would see Alan’s eyes when he tells Manon that she will get hurt if she continues traveling with him, and that we can no longer see them when he brings up—for the first time!—that the reason he doesn’t want her around is because he cannot get stronger with her there, means something. I don’t know how else to explain this or get the point across, but at this point I’m starting to feel like I’m repeating myself, and to be honest, that wears me out. So if you’re still not convinced after all of this, I’d say that it might be best to agree to disagree, because I don’t want to spend all night repeating myself.
That said, here is a recap of Alan’s motivations, all the way up to and including the scene in question:
He started off as Professor Sycamore’s lab assistant. Professor Sycamore was studying Mega Evolution, and Alan himself grew very curious about both Mega Evolution and the theory that the bond between a human and pokémon could have something to do with it. Given that he had already bonded with his Charmander, Alan decided to set out on a journey to research all that he could about Mega Evolution, to see if he could discover something about it for himself, the professor, and the world.
Some time later (enough time for Charmander to evolve into Charmeleon), Lysandre discovered and approached Alan. By this point, Alan was frustrated because he had made absolutely no progress in his research, even though he and Charmeleon had grown stronger as a team. Lysandre revealed that he had a Mega Ring and Key Stone, and offered them to Alan so that Alan could further his research and study into Mega Evolution. The catch was that Alan had to help Lysandre by gathering Mega Evolution energy, which Lysandre told Alan he was going to use for “peaceful purposes.” Alan looked as if he was ~13/14 in the flashback, he was given no reason to think that Lysandre was lying about his “peaceful purposes,” and thought that studying Mega Evolution energy for “peaceful purposes” sounded like a good idea (after all, that’s basically what he was doing before), so he agreed. However, he suggested that they tell Professor Sycamore about their plans, because Professor Sycamore was also researching Mega Evolution. Lysandre quickly shut this down, and said that Professor Sycamore would be in great danger if they told him. If Sycamore knew anything about what they were doing and included it in his own research, then surely people would come to take advantage of him. Alan, being a naive and socially inept young teenager in the face of a grown adult with a silver tongue—and also being immensely protective over those he loves, as well as carrying the fatal flaw of feeling like he has to do everything himself—agrees and immediately cuts himself off from Sycamore.
In other words: I have to stay away from him / he has to stay away from me in order to be safe.
Alan begins studying Mega Evolution, evolving Charmeleon into Charizard along the way and managing to evolve him. This continues until the present, where he is fifteen, and he meets Manon. Manon has just started out on her journey, she’s excitable and clumsy, and while Alan doesn’t mind taking a few minutes out of his day to talk to her, he doesn’t have any intention of bringing her along with him at first. However, Manon decides she’s coming anyway (“You just tagged along without asking …” he says in TSME 4), and Alan allows it so long as she can keep up. (“So long as she can keep up” involves most likely buying her plane ticket to Hoenn, but.)
They end up traveling to Hoenn and discovering the Megalith, which awakens Mega Rayquaza, who is High Key Mad. Mega Rayquaza destroys things, Manon is sent flying by one of its attacks, Alan throws himself through the air to catch and protect her. The entire experience was pretty traumatizing, and by the time Primal Kyogre and Primal Groudon are awakened, Manon is so terrified that she begs Alan not to go, because she doesn’t think it will be safe. Alan agrees that it won’t be safe, but he has to go, so he tells her to stay there, then. Manon, however, is too worried, so she chases after him.
The nigh-apocalypse happens. Alan tries to use Mega Charizard X to fight Primal Kyogre and Primal Groudon, but the fight goes very badly. Charizard nearly dies and Alan himself is knocked unconscious. Manon, who followed along, drags Alan to safety as best she can (I have no doubt adrenaline helped her here), and the two of them are protected by Steven’s Mega Metagross. They probably both would have died if not for Mega Metagross. The situation gets sorted, everyone lives, and Alan feels immensely grateful for both Manon’s assistance and her care. He thanks her, they hug. It’s sweet.
However, that is twice now that Manon has almost died. That is twice now that she has been in grave peril, explicitly because of him. The first time was an accident, but the second time it’s because she was aware of the situation, knew that he would be there, and chased after him. She tells him as much when he asks her if she was scared. We know from how he has responded to Lysandre saying Sycamore will be in danger that Alan has a firm belief that the people he cares about will be in danger if they are around him. It doesn’t matter what causes the danger; Alan knows/feels that he has to go into these dangerous situations, he has to keep pursuing his goal, both because he needs to keep his word, because he needs strength to protect those he loves, and because he believes that Lysandre’s “peaceful purposes” are, well, peaceful purposes that will benefit the world. He can’t stop what he is doing, but what he is doing will put Manon in danger that could get her killed, just like what he is doing could endanger Professor Sycamore if Sycamore gets close, as Lysandre said. Therefore, to keep Manon safe, Alan employs the exact same strategy he employed with Sycamore: He leaves her in Hoenn, tells Steven that he is leaving her in Hoenn because she will not be safe if she is around him, and leaves.
But that doesn’t work. Although he put a literal ocean between them, Manon crosses it to get back to him. He and Charizard notice her during the gauntlet, but Alan pointedly tells Charizard to ignore her, hoping she will take the hint and go away. She doesn’t. When she confronts him, he is at first honest with her; he tells her that she won’t be safe if she’s with him. This doesn’t work either, and she continues arguing and pushing the subject, and that’s when he lies to make her go away. And lo, it worked! She fled, Charizard calls him out on both his lie and the harsh language he used, and Alan says “it’s better this way.” He’s telling himself this so that he will stick to it, so that he won’t go after her and apologize, because if he does that, she’ll go right back to wanting to travel with him, and he can’t have that. It’s too dangerous for her. In Alan’s eyes, it’s too dangerous for him to be in contact with the people he cares about. (And if that doesn’t break your heart at least a little, damn.) The worst part is that he had tried to part on good terms with that hug at the end of TSME 3, because you can tell by the look on his face that he was planning to leave her behind even then, but you know, things rarely go Alan’s way.
Looking at the narrative—looking at everything that built up prior to Alan lying to Manon, as well as the visual cues within the specific scene when paralleled with similar scenes in earlier seasons of the show—it becomes more than obvious that Alan lied to purposefully drive Manon away from him. Saying, “well, he wants to get stronger to protect her, but he can’t do that if she’s there because that’s a distraction, so he was being honest and did mean it” feels more like you’re trying to twist the narrative to suit your interpretation rather than drawing an interpretation from the narrative itself. Alan lied to Manon to drive her away since telling her the truth didn’t work. That he used a lie so convincing that you and Manon both believed it doesn’t change the fact that he was, in fact, lying.
As for a “self-sacrifice” motive, I wouldn’t say it’s that per se, but more that Alan fulfills the tragic hero archetype. He is a heroic character, but he is one whose downfall is routinely brought about by his tragic flaw(s). In Alan’s case in particular, I would name his primary tragic flaw as his insistence on shouldering all burdens by himself and shutting out his meaningful connections/people who could help him, particularly since Pokémon as a series is one that emphasizes teamwork and camaraderie. (This is also why Ash is a successful, standard hero; he has no problem relying on his friends, and this is a lesson he personally will teach to Alan, I believe.) However, Alan is also naive and socially inept as mentioned previously, and this helped Lysandre greatly when it came to manipulating him. Lysandre can manipulate just about anyone, and is a pathological liar to the point where he lies about lying (whether consciously or otherwise), but that doesn’t change the fact that Alan is still far too trusting. For as much as he is a highly competent, skilled trainer, his social intelligence is woefully limited, and that has played a huge part in making him such an easily manipulated pawn.
(Of course, that is also exactly what Malva meant when she called him a “pure boy.” Alan is a pure boy. He firmly believes that he and Lysandre are working toward making the world a better place. He firmly believes he is working toward protecting those he loves. His intentions are pure. It’s his actions that aren’t (namely with regards to helping Team Flare capture Z2), but he doesn’t realize this because he’s being used so effectively. It’s going to no doubt crush him when he realizes the truth, but it’s a lesson he needs to learn, and one that I believe he will learn courtesy of Ash.)
Speaking of Ash, as a final note, it isn’t Lysandre that Alan is “mirroring”—it’s Ash. Alan is a foil of Ash in many different regards, and … I think this was from one of the openings? Or one of the previews, but in any case, the anime team has taken care to specifically point this out:
Two sides of the same mirror, indeed.
