Rune Alchemist
Hey, Rune Alchemist! I know you said you likely won't be able to get to your Homura idea, but some of those are interesting and I thought I would give in my two cents!
I want to mention real quick that crossovers aren't that easy to pull off well and one of the reasons is someone might be unfamiliar with one of the other series's world. I think you're pretty aware of that already, though. Doesn't mean there won't be readers interested in a Madoka/Pokemon crossover as I'm sure there are a few that are!
Thinking about it, I do have ideas. Because of Homura's... stance in Mortality, she would be Immortal, and thus ageless. I thought about having her meet Serena's mother, be best friends with her and two other characters as they travel around a region (I have no idea which one to use yet), and at the end having a falling out at the end of their Pokemon Journey together. Then, several years later, Homura pops up again and meets the main Anime cast (Ash and Friends). A few factors that don't fit is my need for Homura to meet Iris (Which is something that can't change in the story, since it is an important plot point) and Homura meeting up again with Serena's mother.
Curious, why you want Homura to meet with Serena's mother? You think the two will have interesting interactions? Also since you think your idea would fit better during Diamond/Pearl/Platinum story, perhaps it might be better if she meets a D/P/Pt character? Then again, this goes back to your "how do I introduce Homura" question.
I shelved this idea because of a couple of things. One, I'm too busy. One of the worst enemies of writers. Two, I'm already writing a few stories that features her in another world, I need a breath of fresh air. Three, I was thinking of Specializing her, but I can't decide which. I originally had her specialize in Psychic, but then Chandelure and its evolutionary stages are quite symbolic for her. As for Illusions... I'm not too keen about Dark Types, though it does fit her personality. More or less.
I think it's all right to not have all characters specialized in something. Maybe you can just have her very interested in Chandelure and such.
As for my other idea, it's about the Pokemon Conquest Heroine landing in the GamexAnime Verse. In other words, the mainstream Universe. I think I got this idea mostly together. I should have about five arcs for this, namely the "Eevee Arc", the "Modern Arc" (Heroine trying to fit into Modern Changes), the "Descendant Arc" (Where she discovers that she has a Clan under her that survives to this day), the "Pokemon Journey Arc" and finally the "Return to Ransei(?) Arc". The last one has her conflicting whether to stay or not.
I think I can and will write this one, but does it sound like something you'd read?
I don't know much about Pokemon Conquest, so I can't give an appropriate response for that. From what I do know of Conquest it's set in a semi-historical setting, correct? If so I'm assuming you're going for a character from the past and suddenly into the future? The show Sleepy Hollow does a similar premise, so I think it could work and might interest anyone a fan of Pokemon Conquest, the main games, and anime. Only thing I would worry is how well you'll manage the cast of characters from different canons as characters that appeared both in games and anime sometimes have slight different personalities.