Welcome to the board, FullMetalTruth
So, "you can't always get what you want"? (Sorry, watching House
has reminded me I love that song)
The story of two young people facing trials and tribulations in the 'real' world is a very common theme in stories, in anime, in books and shows for teenagers. And in FMA, you're quite right, it is the core of the story. For all that it is expanded (and I'm thinking of the anime-verse) to encompass a range of characters, and huge and abstract theories, BONES/Arakawa wrote a tale centred around two characters developing (with questionable success, IMO) in their world.
The 'genius', if one can call it that, comes from how the story is written. There are bits and pieces of magic, religion, pseudo-science and the conflict between them. And all that gets transmuted into a conflict within individuals and how they relate to world. It is smart, and for a shounen series directed at teenagers it is very smart. Older fans will find nothing new there, nothing ground-breaking that they haven't seen/read/worked out before. But for the younger viewers, there is a new, strong central story there.
On the subject of Ed....granted, he is set up to be something of a role model (after all, he's the main character in a shounen series), but how realistic do you think his point of view really is?
He wavers between moments of revelation, in realising that he cannot understand and control the world through the equations of alchemy to the exclusion of all else, and supreme arrogance in thinking that somehow he can change everything, that all problems are somehow his fault, taking the weight of the world upon his shoulders without consideration of others. One only thinks that if one also believes they can
control everything. Though this does present the conflict Ed faces quite well, I do wonder if it is necessarily realistic, or whether the writers were merely using Ed to express a point of view, as opposed to an actual realistic character.