I think Spike would be a good Frankie like I said earlier. I am not sure who would be a good Usopp to be honest :-/

@Background Pony #2EDB
 
Hence, why i didn’t bother when i have seen Human AJ as Nico Robin, or Twi as Nami and Rarity as Robin or even this particular artist used Octavia and Trixie instead Big Mac and Luna (prefered choices) as Frankie and Brook. Nothing really set in stone, guess what is most interesting is how close MLP characters may react in the same type of situations and scenarios as would the each Strawhat or how well meshed or different the personalities are in comparison.
 
RD and Zoro are different in personality but in their own circle shown as loyalty as all get out. Luffy is having the time of his life an adventure and smiles even if it close to the edge of his own morality, Pinkie Pie is the closest to that and both were pretty much set to despair at the thought of losing their respective friends.
 
Been more of a scenario player than as a visual placement of the characters in my crossovers. It’s cool sometimes how close some characters match up but sometimes come up with different reasons for others that don’t.

@IrieMangaStudios  
Which is exactly why style, appereance, abilities and position in the group should also be considered.  
If we’re going to dig too deep into their personalities, none of the Mane6 fit with their SH counterparts.
 
What part of Dash’s personality fits with Zoro aside from her desire to always win? And even that works in completely different ways. Applejack and Sanji? Its all about the kicking fighting-style. They couldn’t be more different in terms of personality. Rarity and Nami are also complete opposites aside from their interest in fashion (which is only a minor part of Nami’s character, who in fact represents GREED, Rarity’s opposing element).
 
So really, the fact that Spike resembles Chopper in the main and “core” aspects of their beings, should matter more than 1 or 2 personality traits that could go either way.

While Fluttershy may work as Usopp because of the courage thing, she works better as Chopper seeing as she is the only one shown to have any knowledge of medicine/healing. She also usually follows along with everyone else and is sometimes naive and uncomfortable with praise which Chopper is shown to be at times. Chopper also said he would become a monster for his friends that does not necessarily mean you have to become huge to be threatening which Fluttershy more than pulls off.
 
 
Spike as Usopp mostly because Usopp’s signature move is fire and he can take a lot of hits and well Spike is a dragon. Spike likes to play up a crowd and is usually the voice of reason for the main six and Usopp is the most “normal” out of the crew who tells them when they’re doing something crazy or stupid. Both are insecure about their place with their friends and sometimes feel useless. You can also incorporate Usopp’s gluttony and buffness with Spike to give him a more badass look. Finally I can see Spike telling lies and Fluttershy believing them; then the other way around.

@Background Pony #1E59  

 
This was one of the key things that would be OOC for her as Usopp. All are interesting points and even go out as far as the ponies and the Strawhats are not as identical either: RD is not nearly as humble or as stotic as Zoro, AJ is not even close to perverted as Sanji, TS doesn’t have the cool-headedness as Nico Robin, Rarity is more fashionestia than greedy Nami although they both play the dramatics at times.
 
Guess it some of the factors for me was that of scenario situations of characters playing the parts of the different show. Who would play the scene better? FS or Spike in the Luffy vs Usopp fight, Chopper could not bear watching the two go on and wanted to help Usopp’s injuries afterward. And the fact, Usopp gets beat up…A Lot… who is better at absorbing damage? FS or Spike? Chopper gets his share of lumps but when get beat, there are moments of wincing seeing that (the unofficial cute mascot character get beat), not sure if seeing Spike get hit like Chopper would get the same reaction if it happened to Shy.
 
Another scene: who would play it up better? Usopp sniping Spandam from the Tower of Justice and singing his Sniper Song. FS or Spike?
 
But I guess that is speculation and taking the character study lightly or seriously. All as long as the fun of the crossover is still there.

@IrieMangaStudios  
Now I do think you bring up good points on both of them but in my honest opinion, Fluttershy as Chopper mixes as well as oil does with water. While I agree that both Chopper and Shy is into nurturing the key difference between them is that Fluttershy treats animals, not ponies, unlike Chopper who treats people and the occasional animal. And while both Chopper and Shy could seen as similar due to their reclusive nature, the circumstances is very much different, again.
 
Flutteryshy is, by nature, extremely shy around new ponies and she doesn’t handle crowds where she is the center of attention because she is afraid that they will judge her every move and ridicule her.
 
Chopper is more cautious and slighty afraid because of his childhood upbringing. He grew up where even his own herd treated him like a total stranger just because he was born with a blue nose and later as a threat that needed to be destroyed just because he accidently ate a devil’s fruit. And as a last resort he tried to find acceptance among the humans and was treated as a monster. And was feared, hated and ridiculed simply because they couldn’t understand his existance. Of course there was only one (later one more) that saw him, not as a monster, but a hurt and alone creature that needed medical help, Dr.Hiluluk, who became Chopper’s father figure.
 
As for Chopper not doing well when he is the center of attention, it’s not the same as Fluttershy. Because of his childhood, he is absolutely not used to positive compliments thrown his way and reacts like he hates it but contrary to what he says, is giddy as a kindergarden child going to Disney World. He is simply ecstatic when he hears any words of positive reinforcement.
 
Now do I think Spike would be a better Chopper? No, not entirely. I could see him fill the shoe of Chopper’s childhood but it is as you say, Spike lacks the interest in nuturing other ponies/animals and has characteristics similar to Usopp. I guess I could say that I see neither of them fit to play the role of Chopper as they are both missing things that would make them similar to Chopper.
 
As Chopper said to Zoro “Ehehe! I don’t mind! I used to want to be human …but that was just so I could make friends! Now, I’d rather be the kind of monster who can help out luffy!!”

Always thought Spike/Fluttershy and Chopper/Usopp were pretty interchangeable: given Spike and Usopp were treated as the Load/Butt monkey of the group and questioning their usefulness to the group. While Spike and Chopper share the same size and being the different species outside the group, their personalities are pretty different due to Spike was excepted into Pony society while Chopper was a recluse similar to FS. Usopp and Fluttershy are cowardly and show strength when friends are in trouble but Usopp’s bravado and lies don’t really match up to Shy who is more into being nurturing and doesn’t do well when attention is on her (a Chopper personality trait). Seen some Shy as Usopp and Spike as Chopper which were well done, although Spike in Chopper’s clothes (color scheme) kinda clash.

Prefer Chopper.

He should be Chopper, c’mon now.

Meh.  
Its a complete waste not to put him as Chopper.  
The smaller member, the one who’s a completely different race from the others, often seen as the group’s mascot, and with the ability to grow/transform under certain circumstances.

Not sure if he’d be better as Chopper or not…