Something that I thought of which I haven't seen anyone else point out is Alune vs Syndra's situation. They are both in some magical floating fortress. (Syndra "gives" the fortress her power, and the other fortress gives Alune power)
Outside of "white haired girl in temple" there really is little to no similarity between Syndra and Alune. While the temple Syndra lifted up has significance to her, all in all it's a pretty generic temple. Also she in no way "empowered" the temple, she only lifted it telepathically. You don't empower or change objects' properties with telepathy, you just lift em up with your mind. Also, Syndra could've easily snatch a house or something and she can leave her temple if she wants to. This is in no way similar to Alune's situation. For one, Alune's temple isn't "floating", it's in the spirit realm, normal physics don't apply there so to say something can fly or float in the spirit realm would be completely inaccurate. Secondly, Alune can't leave the temple. She's in the spirit realm, if she left god knows where she end up, and that's assuming she has the option to leave anyways.
What I am really trying to say here is that what if Syndra's story continued. She planted her fortress down somewhere maybe or someone was like "hey look up there" and decided to venture in. Good moment to make Syndra more human and less maniacal evil villain. Syndra is power hungry and all but she is still human and this is a perfect time for her to take a break orrr find out whats going on in Ionia considering she is now just a fairy tale to the public...time for her to meet someone. One way or another she gains a disciple --> now she is the master (albeit not a good position for her) who is willing to let her take control. It has been shown she can quite literally take control of whats around her with her dark powers so why not expand that to inbuing it within others as she sees fit.
Yeah no, I want Syndra's story to continue as much as any other Syndra fan but this ain't the way to do it. As Falrein mentioned, her being a master makes no sense since she herself barely understands her powers, she wouldn't be able to explain what and how she's doing what she's doing. Her powers also seem extremely unique to her, it's clearly not normal magic and it's clearly super powerful, I really doubt she could find someone in the world that has similar powers to her. Also, she can't imbue anyone with power, her powers seem 100% destructive, other than her telepathy of course.
Thus "Aphelios" or whatever his new name would be is instead Syndra's foot soldier, gaining information, and just doing whatever while she chills in her castle.
What would be the benefit of this exactly? Aphelios would have his entire personality, his entire existence, dependent on Syndra? I'm sorry, but that's what you call a side character, not a champion. Look at what they did to Senna, before her release she was just "Lucian's wifeTM" but now she's an actual character with her own personality and her own goals. While Senna is teaming up with Lucian, she still isn't completely dependent on him to work as a character and certainly doesn't depend on him being strong. "Syndra's henchman" isn't exactly a compelling character, even if you give him a backstory and personality outside of that, he still won't have his own goals and his powers will still entirely depend on Syndra (assuming you want Syndra to replace Alune). Aphelios and Alune have a much better dynamic, they're both individually strong, but together they work great as a team. Syndra and "Syndra's henchman" would be really pointless since Syndra herself is so ridiculously OP that she would just completely overshadow her henchman.
You could even say "theres a mystical Ionian flower that the monks brewed into tea to resist Syndra's power so that they maintained conscious thought when she tried to project her power onto them, negative side affects include squeezing the throat or whatever" so this new Aphelios can keep his gimmick as a method to stop Syndra's magic from destroying his body.
I don't think you understood the point of the flower in Aphelios' story. He's not drinking poison to "protect himself from Alune's power", he's doing it so that he's so numb that Alune can use the poison as a catalyst to interact with him i.e talking to him and giving him weapons. The poison in Aphelios' story is meant to represent his devotion to both his faith and his sister, he's completely willing to drink extremely painful poison with no hesitation just so he can get stronger to fight for the Lunari AND so that he can talk to his sister again. It just being an anti Alune drug so he isn't destroyed by it takes away from the whole point, in a way it kinda comes off as him rejecting Alune. So no, just keeping the "he drink poison flower" thing isn't enough for his story, the flower itself is meaningless out of context, but it's significant in his lore.
I think Aphelios felt more shoehorned in rather than naturally expanding the faction of Lunari
As a somewhat fan of Aphelios, I disagree. Aphelios did expand the culture of the Lunari. Before Aphelios the most we knew about the Lunari was that they were outcasted (based on Diana's lore) and that they had teachers (Zoe's lore). Outside of a few cameos (like Zoe's teachers, they might've even been the only Lunari we saw pre Aphelios) we never really had any true Lunari. Diana never met Lunari, she just saw the ruins of one of their temples. Aphelios definitely expanded on the culture of the Lunari. They seem completely willing to enforce and raising child assassins and mages, they seem to blend spirituality with their celestial beliefs, with them having a spirit moon and a physical moon. And the most important part, it's implied that the power dynamic in Targon is once again shifting. Aphelios also being the first non aspect human in Targon was a nice change, the Aspects are fun and all but it was about time for some regular humans (or well, as regular as you can get being a league champ).