Okay, so, this has been done a hundred times before by other Thomas/MLP fans but I'd also like to throw my hat in the ring while also having an explanation as to why they correspond to said element. (Think of this as a reflection to the Elements of Harmony, similar to the pillars and the student 6 etc.) (Yes, this was inspired by the Dreamer's Door album from 4everfreebrony) These notes were written for my fanfic "Life Outside" in mind.

Echoes of Harmony:
Henry- Kindness (Benevolence)
Ever since his almost deadly accident with the flying kipper, he's been benevolent. Helping out when he can, keeping an eye out for potential dangers. Although this can make him more stingy about other engine's performances, including his own. Being sensitive to others has helped himself understand more of what matters.

Toby- Honesty (Truth)
Being a hard worker brings out the truth easily out of people, Toby's no different. There's nothing he has to hide, and he won't hide who someone truly is. Though it sometimes gets him into hot water, both his bluntness and his strong work ethic. He won't stand liars and thieves, dealing with both in different ways.

James- Generosity (Selflessness)
He might be vain, self assured and a bit arrogant, but when his positives shine bright, his sharing shows. Generosity in terms of one's self. James' willing to give himself out more than any other engine under pressure. He'll work to the boiler to prove it. If he has more than he needs, he'll gladly give it away, to the most worthy engine of course. It takes a bit of prodding, but his selflessness is truly something special.

Percy- Laughter (Mirth)
Childhood innocence brings the biggest happiness. Percy makes everyone he comes across happier, even when they are annoyed at his naivete. He wants nothing more than to see his friends cheerful. Though sometimes he does have enough of an engine's bs and loves to prank and tease.

Gordon- Loyalty (Allegiance)
Gordon is loyal to his heart. Always wanting the express on time, standing with Sodor even when opportunity for a more glamorous life perks up. Standing by his friends till the end, even if his boastfulness does tend to be hard to listen to; it's often engines take him with a grain of salt.

Edward- "The Spark"
The Spark is the realization.
The realization that you have friends with you, The Connection. It calls upon Magic to being everything together. "The spark" touches each of the elements to realize it so. Magic is kindled by the spark, the feeling of finding a true belonging, a true solidarity. But the Spark only appears when all the elements are present, and then Magic can be formed.

"when the five are present, a spark will cause the sixth element to be revealed."

Edward is the personification of The Spark.
No wonder he's the mediator, the one to bring the best out of every engine, to make them attain a higher level of thought. He's the one who gives the advice. Unfortunately, the spark isn't the one who brings everyone together for friendship. That role belongs to the 6th element.

"When those elements are ignited by the spark, that resides in the heart of us all, it creates the sixth element- the element of magic."

Thomas- Magic (Leadership, Divinity? Still working on the name for this one)
Whenever Thomas is in trouble, or is being wrongfully badmouthed, all the other engines come to support his side. Thomas brings them all together as a unit, and a strong one at that. When a challenge faces them, Thomas is the one at the forefront. Unfortunately, because he is less mature than previous element bearers, the spark of friendship is something he needs represented, hence Edward's place in this particular element group. When worst comes to worst, Thomas buckles down, and rallies his friends together to face it.

I really like this analysis right here.

TBH, all those choices make sense.