@sigh
 
The shipping sprang from the comparison moreso the other way around actually. Outside of being brave when their friends are down or being mocked and cowardly acts, Usopp is not soft-spoken as Fluttershy and Fluttershy does not have the need the characteristics of having being the center of attention. Usopp before being labelled the coward was more known to telling lies, storytelling and being the center of attention to those who would listen to his tall tells as well as being the butt monkey of the group (who takes more physical punishment than anyone in MLP? Spike…).
 
While Chopper and Spike share the transformations, height and off species of the group. Chopper was treated as an outcast while Spike was treated as an welcomed member in pony society. Fluttershy is a bit of an outcast as well. Also Fluttershy has had abit of canon transformations herself (Saddle Rager = Heavy Point Chopper; Flutterbat = Horn/Jump Point Chopper, etc.)
 
The real deciding factor: Usopp versus Luffy - if I had played the scene with MLP with Pinkie Pie as Luffy which character would play Usopp better? Given Spike’s doubt in himself as Humdrum it really cemented the situation when Usopp questioned his own position in the crew, also when Chopper wanted to tend to Usopp’s wounds after the fight parallels something Fluttershy would do. So I went with Spike as Usopp and Shy as Chopper.
 
I could with folks’ opinion of the other way around but this works for me. Besides, plan on an “Fluttershy using an Arm Point (Saddle Rager) versus the Mane-iac in CP9 garb” image soon.

@IrieMangaStudios  
I’m sure the fact that you ship Fluttershy and Chopper together also has nothing to do with it. =P

@IrieMangaStudios  
Heh fair enough. Yup they can be swapped over.
 
Those scales wouldn’t bode well with the hat I’d figure.

@Rotul7
 
I went with Fluttershy’s and Chopper’s nurturing (the media) attributes and awkwardness towards attention. Spike does have some insecurities as well, where his place in the group (Humdrum episode is a parallel to Usopp during the Water 7 arc IMO). Also Usopp being an attention seeker during party times seemed more in tuned to Spike than FS.
 
Either or could be switched though, I just thought Shy wore Chopper’s hat better than Spike.

I always thought, Spike & Chopper were more of the crossover duo, being the different shape shifting monsters that they are.
 
And Usopp more of Fluttershy, being the insecure ones that will always pull through for their friends in the end.
 
I guess they can swap now and then.