Nekiras' alignment has never been definitively established as Evil, whether Diabolic, Miscreat or Aberrant.
BTW, I don't think winged flight should be able to be negated. Or water breathing if the character has gills. Assuming on both of these that they only have one form.
I tend to take this situationally myself.
If the character is a native water breather like Sub-Mariner, then no, Negation is not effective against him, or other Marvel Atlanteans (which is in line with the canon ruling about not affecting aliens with Natural Super Abilities).
If the character has water breathing as a power but is not an Aquatic character, then yes, Negation can and does affect them.
Wings are a tad trickier: generally, I take the position that Negation is (temporarily) inhibiting the bodys' ability to control the extraneous limb (wings, in this case), thus preventing or at least severely restricting flight (in the case of the wings being temporary, they simply fade away for the duration).
The character can glide however, if the wings are in fact still present.
Of course, characters like Lyn-Srial, Phoenixi, Baal-Rogs, Dragons, and other creatures to whom wings are a natural ability are immune to the effect.
when you get right down to it, Sentinel's right.~Uncle Servo.
Sentinel. you'll be always loved by the German Princess.~Nelly
That's twice in one day Sentinel has cleaned up my mess.~The Galactus Kid.
That's the best place to start. Otherwise, listen to Sentinel~lather
Listen to the Sentinel...he speaks truth.~ Shadyslug
Sentinel you have the biggest sig I've ever seen~Natasha