In the matters of crossover...
Soul Society does not understand diplomacy. They are 'supreme', absolute, greedy control freaks, and 'holders of balance' or that crap. They lack rivals and others group to keep them in line.
Many group/organizations/goverments in other shows/animes/series/movies like the Wizard World (both other coutries and families), Vongola, Amestris or even Konoha and Asoiaf has 'other factions' that aren't enemies. They cannot simply do whatever thay please. Soul Society would never let another Spiritual Faction exist outside their control (even if are peaceful doing nothing bad), they would refuse to be 'allies', would demand the other faction to bow or betray them. If they ever 'ally' with an group of another anime/show, they would demand them to be subordinades to Seireitei, obey everything they say and be killed once their usefulness run out. Arrogant at the point of foolishness.
Many 'crossovers' would end up with Soul Society getting in so much trouble because they refuse to talk to solve problem and follow laws and respect the local rulers and leaders, wrongly believing they have authority and jurisdiction over everything and everyone.
The Moral Myopia also. No loyality, no trust, no partnership, nothing. No one would ever want to help them or ally with them, they would try to 'arrest/execute' someone they think is 'different', Ichigo should have noped out of here fast.
Fix-Its with most fandons has politics and talking involved, Bleach ones are about destroying Seireitei cuz Soul Society are a Butch of Motherfuckers.
See Game of Throne for exemple, you have to be careful with no only your enemies, but your allies and subordinades too. Two of Robb Stark's greatest fuck ups are Rickard Karstark (subordinade Lord) and Freys (allies), the Lannisters too (Selmy, the Faith and Tyrion), also which decisions you make and how they affect the other groups (Ned Stark's execution was a reckless foolish action and even Tywin knows it), its so fucking easy to switch sides, your enemies may be more sensible and willing to listen to ours wishes, don't you think so?
This whole 'we have an common enemy' and 'you will help us or else' would never work on many characters like it did on Ichigo and his friends.
No one is going to obey/ally with you if they get nothing in turn/are treated badly/you attempt to make them subordinades instead of allies or something similar. Their attitude towards the Vizards, Bounts, Humans in general or anyone powerful and outside their control tell us an lot. In an crossover, they would attempt to kidnap, interrogate, steal, experiment and murder innocent people with no reason whatsover or commit fucking genocide against societies they consider threats. They did nothing to deserve loyality, refusing to help those who sacrificed so much for them, declaring they own people traitors out of blue (Rukia, Hitsugaya in Diamond Rebellion, fucking Orihime when she got kidnapped) and threatening Ichigo and his friends's often. (Poor Uryu)
I also kinda love the idea where the Hero (an minor, a fucking kid) that has his whole life planned for him to involve himself in an secret world and fight wars that are not his, to put his friend and family in danger for an butch of ungratefull assholes and there is an crossover where said Hero meets people from another Fandom and when the plot starts, he looks the group that wants him to fight for them (and he knows them for like...an hour) dead in the eyes and is like 'lol, nope fuckers, #notmywar, I have better shit to do'.
Its also easier to deal with them. A centralized power that have charisma of lettuce juice (Rukongai would turn against them if given chance), the 'smallfolk' of Soul Society hate then and the Shinigami didn't even try to make some propaganda (like nobles in medieval era giving the rest of the food from feasts so when a rebellion hist, the people would be more willing to hid/help them). Horizontal leadership is more difficult to deal with, independant factions even more.
So yeah, villains like Konoha or Amestris would be far more diffucult to deal with
