Crossovers that shoould be: beginings of Sub Genius

[ECSNorway]

Here's a thought.

Ed finds a Jewel Seed, mistakes it for a Philosopher's Stone.

Ed hooks up with Precia, uses Seed to heal Alicia.

Ed/Precia/Alicia vs Homunculi vs Fate/Nanoha/Chrono...

HAPPY END for Fate (Ed applies Therapy No Jutsu to Precia)
HAPPY END for Ed and Al (Precia clones a new body for Al)

Ed's therapy no jutsu is much different than Naruto's and Nanoha's. He almost never beats somebody until they become better people, instead Ed's therapy no jutsu is almost always "I do something stupidly self-sacrificial for someone who was trying to kill me five seconds ago". Given that, and how Ed reacted to Shou Tucker I don't think "teaming up" with Precia is in Ed's future.
Though how does Nanoha show up? Is this one of the "Precia/Alicia's tube fall through the void of dimensiuons and end up in Crossoververse" stories?
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Epsilon

Point, point. And yeah, that actually works even better.
First season of Nanoha goes pretty much as planned, except that at least one of the Jewel Seeds falls down the rabbit-hold with Precia and Alicia.
Seed+Precia+AliciQ-in-a-can gets found by Ed, at some point in either FMA storyline where he's separated from Al. (Possibly insert Winry going ga-ga over the sophistication of the tech.) Or possibly by some other alchemist, who may have fewer qualms about playing around. Actually, that may work even better. Said person heals Precia using the JS as an alchemical catalyst (maybe it's the priest, whatsisname, Cornello? Or Dr Marcoh?). Precia decides to study this new style of magic and goes off on mad-scientist tangents. Cue Ed, arriving. Cue Ed-Fight.
Somehow, in the fight, Ed gets hold of the Seed, and figures out how to use it. Maybe he figures it's a philosopher's stone, maybe he sees how unstable it is. Either way he knows it's not a good idea to depend on it... But he sympathizes with Precia's motives (not knowing of Fate's existence nor of Precia's treatment of her), and burns out the Seed using it to alchemically heal both mother and child. (Alternatively, he persuades Marcoh to perform the healing, with a rather passionate expostulation on the importance of family, motivated by his own tragedy...)
At this point ideas diverge. We've already seen a story where Precia and Alicia settle in with the locals of the crossverse (Naruto, in that case) and become valued allies of the heroes there. It can work in FMA, but it then sets up a situation where Nanoha et al show up eventually and come over all imperious trying to arrest the former criminal.
In this case, we've got a built-in cast split already, with the FMA story going in several directions at once. Burning out the Jewel Seed sends a ripple through the Dimensional Ocean, and Nanoha & Fate are sent to investigate. They end up working with one group (perhaps Roy Mustang? A not-in-StrikerS-yet Nanoha would probably get along pretty well with him...) while Precia and Alicia follow another, and it's entirely possible that some third Nanoha-verse faction ends up involved as well (is Jail Scaglietti supplying technical know-how to some faction? Maybe working with a renegade alchemist, like Kimblee?)
Things go on like that, with each group hearing bits and pieces about what's going on with the others but none of the Nanoha cast quite getting the chance to find out just who the other group from their end of things is... until near the climax, where we have a nice big Befriending, and the united group sets off to challenge Le Big Bad in his lair.
How's that so far?
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Sucrose Octanitrate.
Proof positive that with sufficient motivation, you can make anything explode.