This has been brought up before. There are some distinct similarities between the two, but they're superficial and I'm sure they're coincidental. The idea of a living suit of armor is well-rooted in the fantasy genre. The idea of a character being preserved in a living suit of armor isn't outlandish enough of a concept to have to have been inspired by Fullmetal Alchemist. The trains appearing along with the soul bonded to armor is a little significant, but again it seems there were other reasons for picking the trains and the trains were a side element in FMA... no not even a side element. They were utterly insignificant. Only real form of land transportation in a period like that.
Another small thing I thought was that both Link and Ed are in a way short. Even though a lot of the people in ST make that size normal it still seems kind of short to me. You know Alfonzo from ST,well doesn't he brag a little about his family like Armstrong from FMA. They both seem to have Large - what am I saying?!, Armstrong's muscles are HUGE! But sill they do seem to be alike. How about Anjean from ST, isn't she a lot like Teacher or Izumi. They both teach Link and Zelda, Ed and Al about Energy and Life.
Link has always been that short. That similarity means nothing really. Besides, Link is actually a small child and other kids are shown to be his height, so he's not unusually short like Ed is (and if you go to the manga or the new anime, it shows that Ed is short unnaturally because he's eating for both himself and Al's body). I don't remember Alfonzo bragging much really, and his size (and design, really) is identical to Gonzo in TWW and PH really so that's not intentional. Anjean and and Izumi aren't really similar at all either. Izumi teaches Edward and Alfonse philosophical lessons about life and energy and the way of the world, whereas Anjean kinda casually explains how the energy seals Malladus. Izumi was also a unique character whereas Anjean was a bit more of a "wise old man/woman" kind of archetype.
Don't you think Byrne from ST is slightly like Scar from FMA? Scar didn't want this thing happen to him,but this power he has is like Byrne's power. Byrne also performs an act like Scar that really affects the story. Scar creates the Philosoper's stone and byrne leads them to the Ligh arrow.
I'll admit both Byrne and Scar are alike... in one aspect only though: Their character archetypes. They're the same basic concept, one that is pretty overused, so there's nothing special about that connection either. Additionally, I really wouldn't compare the Philosopher's Stone with the Light Arrows. The Light Arrows are a special weapon designed to defeat evil sealed in a temple. The Philosopher's Stone is a powerful force that requires horrible sacrifices of human lives to create and allows the user powers like creating life and breaking the laws of nature. It's as much of a sinister force as it is the ultimate goal of the protagonists. The Light Arrows are just the means to the ultimate goal of the protagonists.
