My thoughts about it.
It's quite not "The Nile Empire is Better at Everything" as it is. It's "The Nile Empire is Better at Everything that matters for particular character (exclude psi)". And also Nile Empire isn't actually limited - it's too close to Core Earth socially and axiomatically.
If you want to create powerful miracle worker - you can take Living Lands character, who would not be able to use automatic weapons and will not understand conception "it's not good to just take a meat in this strange glass box", because idea of store, money and unpersonalized trade is contradictory for him (yup, as a reality-rated character he can be teached, and it would be just 1/20 variable he would disconnect every time he is hungry and doesn't just break in meat store). Or you can take Nile character with Super Faith and Super Spirit, who is, well, just very good priest from pulp realm, with some kind of story. Thing is, every reality-based character should have a story, after all.
If you want to create powerful sorcerer - you can take Aysle character who would have some spells, but still would be a man from high fantasy realm, and, well, there is no some very powerful spells only Aysle can take (and it wouldn't be until Aysle book, right?). Nile can take Spellcaster and Super Favored School, so, as Spellcaster would give him 3 spells like Aysle one. Nile spellcaster would be limited by spell list, but Nile spell list is actually good spell list (and that's just Core book I'm looking into now).
In a nutshell, if you want to create a man who doing something good, Nile actually is the realm created for such characters. And he isn't bad in all other things, right? I mean, perks and stuff is for specialization; and Nile is the best for specialization, because cosm IS for specialization.
So to fix it I'd nerf Nile perks by doing one Limitation set mandatory, and second for enhancement if player want one. Every Nile perk should be limited. It's what exactly what pulp characters are, after all - they have powers, but this powers are innate unreliable. You always have this pulp guys as something strange, they have their limitations and stuff, and their tech explode.
I argue fiercely, but I never believed disagreement should be capital offence.
I'm editing my posts often. English isn't my native language, and I'm doing a lot of mistakes; that, with thoughtful rereading, I often found and want to edit.