Originally from this post in the '[NSFW] Gender Bend Fic Discussion, Idea, Rec. thread,' also at QQ:

• Kämpfer, but:
  • With a number of the changes suggested in: https://www.youtube.com/watch?v=vDthshhgcZ4
  • Better setup for the Moderators, though I haven't come up with what that might entail, if anything. The threat they pose doesn't turn out to have felt too serious in canon?
  • At least slightly deeper focus on how Natsuru handles adjusting to his sex swap, particularly in terms of:
    • him having a tad more control over how she ends up presenting herself,
    • actual partial reasoning for how she ends up acting as a girl even if its along the same lines as in the source material, or
    • some of both.
  • Better setup, payoff, and/or use for/of some lines, namely:
    • Natsuru's 'I feel dark' one (can't remember the exact wording) from…maybe episode 3, I think? It was when she was forced to dress up in some costumes at school.
    • Natsuru's offense at Mikoto's secondary reaction at finding out that he's a Kämpfer delivered when they retreat to a room to discuss it. (It struck me at the time I watched that part that this could have gone more like 'Hey, it's not like I asked for this!')
• Cheeky Angel, but the incident that changes Megumi into a girl in the first place isn't by finding that sorcerer's book with a trickster genie inside, but instead one around the same time where her friend Miki, who knows he was once a boy after the fact either way, got held hostage and Megumi had to turn into a magical girl to save her, getting stuck female both in and out of transformation afterward. (Though I don't know what enemies she could fight.)
• Ame Nochi Hare (Clear Up After Rain,) but the initial lightning strike doesn't start the characters flip-flopping sex to female when it rains until the change wears off and instead makes always-girl copies of them appear.
• Princess Princess (including Princess Princess Plus,) but the 'princesses' of each cardinal compass direction actually live in a dorm that way from the school, all of which have magical elements that occasionally select candidate males from their resident populations to take on the duties of magical girls.
• Reversible, a. k. a. Reversible School Life, but the students actually become girls instead of just crossdressing.
• Either or both of the following, but the students actually become girls instead of just crossdressing:
  • Reversible, a. k. a. Reversible School Life
  • Armed Girl's Machiavellianism
• Nozomu Nozomi, but changed to resolve the critique from this mostly on-point MyAnimeList review.
• A gender-bender multi-crossover, involving at least some or all of:
  • Kämpfer (either canon or the fanfic idea above.)
  • The Cheeky Angel fanfic idea above.
  • The Princess Princess fanfic idea above.
  • Shishunki Bitter Change
  • Boku Girl
  • Maybe Click?
  • Kanaete Aizen, or Grant My Wish Aizen
  • Maybe Kashimashi: Girl Meets Girl.
  • The Nozomu Nozomi fanfic idea listed above.
  • Maybe Osananajimi wa Onnanoko ni Naare.
  • May-be Akane-chan Overdrive?
  • Maaay-be Boku wa Mari no Naka, or Inside Mari, but without the twist revealed at the end. (I don't know if you could make a stand-alone fan fic out of this, so I didn't list it earlier.)
  • Perhaps Doll-Kara.

(You'll note I stuck with male-to-female — 'Males Cross-dressing,' 'Swap,' 'Male Beocmes Female,' and 'Male in a Female's Body' — entries from the MAL forums 'Organized list of gender bender/swap anime and manga' thread, and those that have gender-bending as a main focus not really sharing the spotlight with something else plot-heavy besides, but I suppose you could do what you wanted here. Anyway, characters would run into each other at points even if they didn't get involved in each other's/others' stories, and perhaps a support group for transformees might crop up?)

(Edit: The part of this which should've stayed quoted was previously in a block quote, but that eliminated some distinctions in italicization, so I replaced said block-quoting with delimiters in the form of horizontal line rules. Also edited a few times to fix some copy-paste errors introduced into the post's formatting when manually converting it over from the original BB code source to the limited HTML used here on the forums.)