One reason Homura is doomed to suffer is that her relationship with Madoka is built on a fundamental paradox. Homura loves Madoka for her kindness, her compassion, her willingness to save others, all of which are epitomized by their first meeting at school and again when Madoka saves Homura's life. At the same time, those exact same traits are what pull the two of them apart in every single timeline, as Madoka's kindness, compassion, and drive to save others drive her to her death.
Homura fights Walpurgisnacht in order to save Madoka, yes, but in a very real way, she's also fighting against Madoka's fundamental nature, and she can never, ever, win, as the ending of Rebellion proves. No matter what the circumstances, these are Madoka's core traits, the ones that define her as a person (consider how in the flower field scene, Homura identifies Madoka as the real thing by her "kindness" and "warmth" as opposed to literally any other traits). If by some magic, Homura could erase them, the girl that emerged wouldn't be Madoka anymore, just a stranger with her face and voice.
That in itself would be enough to induce complicated feelings in any relationship, but it gets worse because of Homura's lack of self-esteem: she doesn't feel she is worth saving. Her reaction to Madoka's first death in the original timeline is telling: "Why? Even if you were going to get killed all along, it wasn't worth saving me if you're not alive!"
The third timeline is even more explicit, with Homura envisioning a world where she and Madoka are together forever as witches, where Homura's abnegation of self and her love for Madoka could find a stable balance that would never be overturned--and Madoka rejects it completely and irrevocably, without any warning whatsoever.
Instead, she asks Homura to go on living without her because Homura can go back in time. People are usually focused on the part where Madoka asks Homura to save her personally, but before that Madoka asks her to "change everything... so we don't end up like this". The "we" here is ambiguous, but Madoka also means Mami, Kyouko, and Sayaka here, not just her and Homura. (Remember, this version of Madoka murdered Mami to save Homura, and has been understandably traumatized by it!) And not only does Madoka reject Homura's offer to die together, she also rejects Homura's worldview completely--stating explicitly the world is worth saving, in spite of the horrors--and asks Homura to kill her in order to prevent the very fate that Homura advocated for them both just moments ago (i.e, becoming a witch).
This is, in my opinion, one of the most pivotal scenes in the entire show, the one that catalyzes Homura's worldview, that changes her life, that transforms her utterly, that is so deeply seared into her psyche she can never let go of it (as we see in the climax of Rebellion). The fandom tends to focus on the grief and guilt and self-loathing, which is obviously a huge piece of it, but you can also see in that moment why Homura might hate Madoka for it, too: for saving Homura's life once again instead of her own, when Homura didn't want it; for forcing Homura to keep on living and fighting in order to see her again; for asking Homura to mercy-kill her (the one thing that traumatized Homura more than anything else she ever experienced).
Over and over again, Madoka keeps leaving Homura behind, and it's perfectly understandable why Homura might resent that, why she might hate it, and hate Madoka for doing that to her, even though she loves Madoka, because the things that she loves about Madoka and the things that she hates about Madoka are fundamentally the same. This is what I think the concept movie trailer was getting at with its references to "that cruelty, that gentle radiance", which also appears in the WnK trailers as "a radiance so kind, that it is even cruel".
Rebellion explicitly states that love and pain are intertwined for Homura, and I think all of the negative feelings Homura might have for Madoka are a part of that, even though Homura will never (consciously) admit to them. It's one reason why the Clara Dolls, those avatars of Homura's unconscious, are throwing fruit at the Madokami stele while Homura worships it--on some level, she hates Madokami even as she loves her (because she loves her), but those negative feelings are suppressed and acted out via proxies instead.
You could argue that Homura doesn't actually hate Madoka, just the Madokami part, but what exactly is the difference between them? Homura's rebellion is predicated on the assumption that she can remove the girl from the Law of Cycles, but instead of getting the same reaction from the flower field scene, Homura discovers that she can't remove the impulse that created the Law of Cycles from the girl--simultaneously the trait she loves most about Madoka and the one she's been fighting the whole time! The primary differences between amnesiac human Madoka and Madokami are ones of power and agency, not kindness and compassion. No wonder Homura is in hell.
The irony, of course, is that so much of Madoka's self-sacrificing tendencies are driven by her own lack of self-esteem and self-worth; she is not so different from Homura in that respect. However, from Homura's perspective, Madoka is enough as she is because Homura loves her, hence Homura repeatedly telling her she doesn't need to change; Madoka's relationships to her family, friends, and most especially Homura, are enough to justify her continued existence. In context, this request to "not change" is about Madoka becoming a magical girl or not, but on a larger level, Homura is asking for the impossible: in order to be the sort of person who could "stay the same" the way Homura wants, Madoka would have to already be someone other than who she is!
At the same time, Homura's inability to let go is her core trait and Rebellion ends with her doubling down on it. In order to be the sort of person who could "move on", Homura would also have to become someone completely different, and I genuinely don't know if that's possible. [In real life, absolutely, but characters are not real people, and it's hard for me to imagine Homura without her core traits, just like its hard for me to imagine Madoka without hers.]
Okay, so if changing Madoka and/or herself is off the table, what other course is left to Homura? Well, if the world is such that Madoka feels compelled to sacrifice herself, maybe change the world so she doesn't have to. This is what Homura was trying to do by defeating Walpurgisnacht by herself, but even if she'd succeeded, it would have only been a matter of time before something else happened and Madoka was compelled to do something about it. (In the PSP game, there's a scenario where Homura manages to win, although she dies in the process, and Kyubey is like, "well, that didn't work out, but I'm sure something will come up that will make Madoka want to contract and I'll be right there when it does".) And becoming the devil also changed the system, but not enough - Madoka comes perilously close to reverting right in front of Homura's eyes.
One solution is to destroy the Law of Cycles permanently, so that Madoka can never rejoin it and leave Homura behind again. This is bad for everyone else for obvious reasons, but it would allow Homura the opportunity for a do-over on the whole "become witches together" offer that Madoka rejected the first time around. This is something that the original Homura is (probably) not ruthless enough to go through with, but I suspect the other Homura might find it an ideal solution. TBD.
Homura and Madoka coexisting as concepts sounds great, except for the fact that their current concepts are mutually exclusive, to the point that I'm not sure it's possible for both divine forms to exist at the same time. Maybe this isn't the case, and it's fine, but I don't know how it would even work - Madokami doesn't need a counterbalancing devil, and the devil set up her entire system explicitly to keep Madokami out of it, so it doesn't seem like there's much room for coexistence there.
What Homura and Madoka really need is a new system, something that will allow Madoka to save people (either without dying or because she's reached an end state where death/change is no longer possible), and Homura to stay with her forever - a world where each of them can be happy without sacrificing their core traits for the other, perhaps as a new kind of being that doesn't exist yet. They have to be together, they have to be equals, and they have to be inseparable for any kind of long term stability. That's a tall order, but I think it's possible - but only at the end of a long, circuitous, and increasingly improbable road that creates the exact set of circumstances necessary for its creation.
Or at least I hope so, because that's the good end. We already had the end where Homura failed and kept on going (original anime), and the one where she technically achieved her goal, only for it to slip away from her (Rebellion), so the only options left are to change, to die, or a secret third thing. I'm not a betting person, but given the odds and Urobuchi's general theory of character development, I'm placing my hopes on a secret third thing.
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