My picks:  
Spike is Thomas  
Doctor Whooves is Edward  
Wensley is Henry  
Flash Magnus is Gordon  
Feather Bangs is James  
Pipsqueak is Percy  
Mr. Waddle is Toby  
Twilight Sparkle is Emily

@EndlessWire94  
Also, if Gilda hadn’t changed her ways, she might have been a good match for Vinnie from The Great Race.

Come to think of it, Rainbow Dash is kind of similar to Duncan from the Skarloey Railway, considering they both tend to be “plain and blunt”.

@HamburgerTime  
Fluttershy would be good as Stepney. Think about it: Stepney works on a line surrounded by bluebells, and Fluttershy likes to surround herself with nature.

Diesel is the new Trixie, not Gilda

Sir Topham Hat.
 
WHY DO I REMEMBER THIS, I WAS FUCKING SIX YEARS OLD

Hey, that’s an insult to Diesel. He may have had a short temper, but he was somewhat clever in his bullying. Gilda’s just a brute.

Henry, you’re the new Gordon.
 
Also Celestia should be Sir Fathead.
 
And why is Fluttershy Duck? Duck isn’t shy, he sent Diesel packing and braved a snowstorm to help Toby save some sheep!

ding ding  
doodiedoodiedoodiedoodie  
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doodiedoodiedoodiedoodie dum
 
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And Applejack should be Edward.

Dash should be James (for obvious reasons), Rarity should be Henry because they have both have had hussy fits about going in the rain. Fluttershy should be Terrence, and spike should be Percy.

Henry has always been WAY, WAY, more useless than Spike has ever been. That and Pinkie may be a bit of ditz but she’s not nearly as stupid as Percy is.