Exec: ….Gaudier
 
Designer: Sir, I can’t-
 
Exec: GAUDIER!
 
Designer: But it’ll look horr-
 
EXEC: GAUDIERRRR!

@Background Pony #10ED
 
There’s actually no official confirmation of such a thing — at least as far as I know.
 
Did the change happen early or late in the development of the toyline (and by extension the movie and shorts)? If the latter, would probably explain why Indigo looks like Lightning. If it had happened early, they could’ve changed her design.
 
Would be nice to know what happened with the Lightning Dust-lookalike doll, and why was it changed. It’s just one of those weird mysteries…
 
The Shadowbolt School Spirit proto-dolls actually look very different from the finished product, unlike the School Spirit (Wondercolt) or Sporty Style (everyone but, uh, Indigo Dust).

@Ultra64  

 
That because she WAS supposed to be Lightning Dust originally, but Hasbro decided to recolor her for no good reason.

@SJArt117
 
Really, I love Indigo’s toy design. The major gripe I have with her character design in the movie is that she looks just… Way too much like an humanized Lightning Dust — it bothers me.
 
 
@lunafan22
 
As confirmed by her Sporty Style (or whatever) doll.

so indigo is a pegasus?

Took me a while to realize that was AJ between Twilght and Indigo. She looks very different with that hairstyle.

Indigo Zap looks so much better in this.  
Maybe not so with the pink skin, but definitely a better hairdo and colour scheme there.